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Annotation of /pkg/ChangeLog

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1 : bates 1405 2006-08-21 Douglas Bates <bates@R-project.org>
2 :    
3 :     * src/lmer.c (internal_mer_RZXinv): Fix memory leak caught by
4 :     valgrind.
5 :    
6 : bates 1403 2006-08-20 Douglas Bates <bates@R-project.org>
7 :    
8 :     * src/sparseQR.c: Fix thinko in sparseQR_resid_fitted.
9 :     * tests/sparseQR.R: Added
10 :     * man/sparseQR-class.Rd: Document methods for qr.* generics
11 :     * R/sparseQR.R: Return correct # of coefs; fix cut-and-paste errors
12 :    
13 : bates 1398 2006-08-19 Douglas Bates <bates@R-project.org>
14 :    
15 :     * NAMESPACE, R/sparseQR.R, src/init.c,sparseQR.[ch],SOURCES_C.mkf:
16 :     Added methods for sparseQR for qr.qy, qr.qty, qr.coef, qr.resid
17 :     and qr.fitted.
18 :     * src/Mutils.[ch]: Added dup_mMatrix_as_dgeMatrix utility
19 :     * src/dgCMatrix.c: Check for ordering before storing q in dgCMatrix_QR
20 :    
21 : maechler 1389 2006-08-18 Martin Maechler <maechler@stat.math.ethz.ch>
22 :    
23 :     * R/AllGeneric.R: add "qr" and "chol" generics; via 'trick' since
24 :     the base version has no "..." argument.
25 :    
26 :     * R/sparseMatrix.R (prSpMatrix): fix the triangular unit diagonal case.
27 :    
28 :     * R/Matrix.R: define and
29 :     * NAMESPACE: export as.numeric() and as.logical() methods.
30 :     Let's hope these do not badly slow down something...
31 :     Finally export the zapsmall() method.
32 :    
33 : bates 1388 2006-08-17 Douglas Bates <bates@R-project.org>
34 :    
35 :     * src/dgCMatrix.[ch] (dgCMatrix_matrix_solve), src/init.c,
36 :     R/dgCMatrix.R: solve methods for dgCMatrix and dense RHS.
37 :     * src/dtCMatrix.c :Remove code that is no longer used
38 :     * R/dtCMatrix.R: Use C code for diagU2N in CsparseMatrix classes
39 :    
40 : bates 1370 2006-08-14 Douglas Bates <bates@R-project.org>
41 :    
42 : bates 1373 * src/Csparse.[ch],init.c (Csparse_to_logical): Added utilities
43 :     Csparse_to_logical and Csparse_symmetric_to_general.
44 :     * R/dgCMatrix.R,dsCMatrix.R,Csparse.R : Consolidate general
45 : maechler 1389 coercion methods between CsparseMatrix and TsparseMatrix.
46 : bates 1373
47 :     2006-08-14 Douglas Bates <bates@R-project.org>
48 :    
49 : bates 1370 * R/dtCMatrix.R,dgCMatrix.R,Csparse.R src/init.c,dgCMatrix.[ch],
50 :     Csparse.[ch],chm_common.c,dense.c : Use CHOLMOD code and methods
51 :     for CsparseMatrix, TsparseMatrix, denseMatrix or matrix when
52 :     possible.
53 :    
54 : bates 1368 2006-08-12 Douglas Bates <bates@R-project.org>
55 :    
56 :     * src/chm_common.[ch],Csparse.[ch],Tsparse.[ch],CHMfactor.c,dtTMatrix.c,
57 :     dgTMatrix.c,dgCMatrix.c,dsCMatrix.c,dtTMatrix.c, R/dsTMatrix.R,
58 :     Tsparse.R,Csparse.R,dgTMatrix.R,dsCMatrix.R,lsCMatrix.R:
59 :     generalize conversions between TsparseMatrix, CsparseMatrix,
60 :     denseMatrix and matrix. Preserve triangularity property and
61 :     propagate Dimnames in the easy cases.
62 :    
63 : bates 1365 2006-08-10 Douglas Bates <bates@R-project.org>
64 :    
65 :     * src/lmer.c: adjust checks in glmer_init for S4SXP
66 :     * tests/validObj.R: check of all(eq) should be all(eq@x) - worked
67 :     before S4SXP but for the wrong reasons.
68 :    
69 : bates 1354 2006-08-08 Douglas Bates <bates@R-project.org>
70 :    
71 : bates 1360 * src/Csparse.c (Csparse_crossprod): tcrossprod result has stype = -1.
72 :     Later modified to return the upper triangle only.
73 :     * R/dgTMatrix.R: Remove vestigial crossprod and tcrossprod methods.
74 : maechler 1389
75 : bates 1352 2006-08-07 Douglas Bates <bates@R-project.org>
76 :    
77 :     * src/Csparse.c (Csparse_crossprod): Set stype on result to avoid
78 :     R-level conversion to a sparse symmetric class.
79 :     * R/Tsparse.R,R/Csparse.R (crossprod and tcrossprod methods):
80 :     Remove conversion to sparse symmetric classes (now done in C code).
81 :    
82 : maechler 1349 2006-08-07 Martin Maechler <maechler@stat.math.ethz.ch>
83 :    
84 : maechler 1351 * R/dgCMatrix.R: disable old crossprod and tcrossprod methods
85 :     * man/band.Rd: adapt the \dontshow{} unit test.
86 :    
87 :     2006-08-07 Martin Maechler <maechler@stat.math.ethz.ch>
88 :    
89 : maechler 1349 * DESCRIPTION (Version): 0.995-14 for CRAN
90 :    
91 :     * tests/other-pkgs.R: oops: library(Matrix) outside *if* !
92 :    
93 :     * R/sparseMatrix.R (Tsp2grNEL): fixed Tsparse -> graph coercion
94 :     * tests/other-pkgs.R: more checks, sparseMatrix -> graph
95 :    
96 :     * R/Auxiliaries.R (as_Tsparse, as_Rsparse): new
97 :     * R/Tsparse.R (tril, triu, band): methods
98 : bates 1352 * R/dgRMatrix.R (tril, ...): ditto
99 :     * man/band.Rd: ditto
100 : maechler 1349
101 :     2006-08-04 Martin Maechler <maechler@stat.math.ethz.ch>
102 :    
103 :     * R/Matrix.R (head, tail): directly use utils:::head.matrix
104 :     to be up-to-date automatically.
105 :    
106 : maechler 1346 2006-08-03 Martin Maechler <maechler@stat.math.ethz.ch>
107 :    
108 :     * DESCRIPTION (Version): 0.995-13 to be released to CRAN
109 :    
110 :     * DESCRIPTION (Lazydata): no, instead of 'yes' because it fails for:
111 :     * data/CAex.R, inst/external/CAex_slots.rda: replacing data/CAex.rda
112 :     * data/KNex.R, inst/external/KNex_slots.rda: replacing data/KNex.rda
113 :     such that the S4 objects are always created by the current version
114 :     of R and 'Matrix' class definitions.
115 :    
116 : bates 1342 2006-08-01 Douglas Bates <bates@R-project.org>
117 :    
118 :     * R/lmer.R (LMEoptimize method), tests/lmer.R,
119 : maechler 1346 inst/external/test3comp.rda: Added warnings for convergence on
120 : bates 1342 boundary and test cases.
121 :    
122 :     * src/lmer.c (mer_postVar): Modified to return the variances that
123 :     are marginal to the fixed effects, not conditional on them (which
124 :     is what the bVar slot contents represent).
125 :    
126 : bates 1338 2006-07-31 Douglas Bates <bates@R-project.org>
127 :    
128 :     * NAMESPACE, src/lmer.c, R/lmer.R (hatTrace): Add the hatTrace
129 :     function which calls the C function mer_hat_trace2.
130 : maechler 1346
131 : bates 1342 * man/ranef.Rd: Include description of "postVar" argument and
132 :     producing a caterpillar plot.
133 : bates 1338
134 : maechler 1335 2006-07-31 Martin Maechler <maechler@stat.math.ethz.ch>
135 :    
136 :     * NAMESPACE: change "correlation" to "corMatrix"
137 :     * R/AllClass.R: to avoid clash with S3 class in 'nlme'.
138 : bates 1352 * R/dpoMatrix.R: ditto
139 :     * R/lmer.R: ditto
140 : maechler 1335
141 : bates 1338 2006-07-28 Douglas Bates <bates@R-project.org>
142 :    
143 :     * src/lmer.c (internal_mer_RZXinv): Split the calculation of the
144 :     RZXinv slot's contents into a separate internal function that can
145 :     be used in mer_hat_trace.
146 :    
147 : maechler 1331 2006-07-22 Martin Maechler <maechler@stat.math.ethz.ch>
148 :    
149 :     * R/Matrix.R: Coercions "Matrix" -> (sparse|dense)Matrix
150 :     via new smart
151 :     * R/Auxiliaries.R (as_Csparse, as_dense, .M.shapse): new
152 :     utility functions.
153 :    
154 :    
155 : maechler 1330 2006-07-21 Martin Maechler <maechler@stat.math.ethz.ch>
156 :    
157 : maechler 1331 * R/Csparse.R (tril, triu, band): do return *triangular* classed
158 :     matrices when appropriate; band() even symmetric ones.
159 :     (replCmat): extend to potentially all "CsparseMatrix"
160 :     * R/Tsparse.R (replTmat): extend to all "TsparseMatrix"; hence
161 :     allow subassignment for special sparse matrices.
162 :    
163 :     * R/Auxiliaries.R (as_geClass): factor out the .M.kind() functionality
164 :    
165 : maechler 1330 * src/lmer.c (mer_MCMCsamp, glmer_MCMCsamp): new 'verbose'
166 :     argument; in glmer_*(): print only if(verbose).
167 :    
168 :     speed-optimize a few places by moving REAL(.) out of loops.
169 :    
170 :     * src/lmer.h, src/init.h, R/lmer.R: related to above.
171 :    
172 : maechler 1329 2006-07-20 Martin Maechler <maechler@stat.math.ethz.ch>
173 :    
174 :     * R/Matrix.R("["): disable ("Matrix", i = "logical", j = "missing"),
175 :     since that wrongly triggers also for M[ logi , ]
176 :    
177 :     * R/denseMatrix.R: "[" methods now also work e.g. when indexing
178 :     a symmetric matrix that results in a non-symmetric one.
179 :     * R/Auxiliaries.R (as_geClass): new function used in "[" above.
180 :    
181 :     * R/dMatrix.R: make round(M) work as round(M, 0)
182 :    
183 :     * R/dgTMatrix.R (image): coordinate system and axis now use
184 :     1-based indices, not 0-based ones.
185 :    
186 :     * R/Tsparse.R (.ind.prep for "["): get rid of max(<empty>) warning.
187 :     * tests/indexing.R: test it.
188 :    
189 :     * NAMESPACE: export isSymmetric(); has been a generic in "base" for a while;
190 :     * man/isSymmetric-methods.Rd: and document it.
191 :    
192 :     * R/SparseM-conv.R: added coercion methods for some 'SparseM' matrices.
193 :     * man/SparseM-conv.Rd: docu them
194 :    
195 :     * tests/other-pkgs.R: renamed from tests/graph.R and add example
196 :     for 'SparseM' conversions
197 :    
198 :     2006-07-17 Douglas Bates <Douglas.Bates@R-project.org>
199 :    
200 :     * R/Matrix.R (head): added head() and tail() methods.
201 :    
202 :     2006-07-17 Martin Maechler <maechler@stat.math.ethz.ch>
203 :    
204 :     * DESCRIPTION (Version): 0.995-12 released to CRAN
205 :    
206 : maechler 1319 2006-07-15 Martin Maechler <maechler@stat.math.ethz.ch>
207 :    
208 :     * tests/simple.R: add check for correct dsT -> dgT coercion;
209 :     add check for correct printing of symmetric sparse matrices.
210 :    
211 :     * R/Auxiliaries.R (non0ind): return *all* non-0 entry indices also
212 :     for sparse symmetric matrices.
213 :    
214 :     * src/dsTMatrix.c (dsTMatrix_as_dgTMatrix): do not copy the
215 :     diagonal twice.
216 :    
217 : bates 1316 2006-07-11 Douglas Bates <Douglas.Bates@R-project.org>
218 :    
219 :     * src/dsTMatrix.c (dsTMatrix_as_dgTMatrix): Fix a case of INTEGER
220 : maechler 1319 being applied to the x slot (detected by Brian Ripley).
221 : bates 1316
222 : maechler 1315 2006-07-10 Martin Maechler <maechler@stat.math.ethz.ch>
223 :    
224 :     * src/dgCMatrix.c (dgCMatrix_validate): 'p' slot must have correct length.
225 :    
226 :     * R/Auxiliaries.R (isTriC): fix buglet (we were 1-based!)
227 :    
228 :     2006-07-08 Martin Maechler <maechler@stat.math.ethz.ch>
229 :    
230 :     * src/lgCMatrix.c (lgCMatrix_diag): new function
231 :     * R/lgCMatrix.R (diag): for new method
232 :    
233 :     * R/AllClass.R (TsparseMatrix): do use Tsparse_validate
234 :     ==> construction of illegal "*gTMatrix" via new() should
235 :     now be much less easy:
236 :     * tests/Class+Meth.R: assertError() for some illegal "dgT*"
237 :    
238 :     * R/Matrix.R (Matrix): Matrix(0, nrow,ncol) now "goes sparse"
239 :     directly.
240 :     * man/Matrix.Rd: documents it.
241 :    
242 : bates 1311 2006-07-06 Douglas Bates <bates@R-project.org>
243 :    
244 :     * src/pedigree.c (pedigree_inbreeding): Correction in
245 :     initialization. This function is not currently being used and is
246 :     not fully tested.
247 :    
248 : bates 1312 * NAMESPACE, R/{AllClass.R,lmer.R}, src/{init.c,lmer.c}:
249 :     Introduced the glmer class. Added code for mcmcmsamp on glmer
250 :     objects. Modified validity check on pedigree objects to account
251 :     for nonparallel patterns of missingness of parents.
252 : bates 1311
253 : bates 1313 * man/{lmer-class.Rd,mcmcsamp.Rd}: Update documentation for glmer
254 :     class.
255 : maechler 1315
256 :     2006-07-01 Martin Maechler <maechler@stat.math.ethz.ch>
257 :    
258 :     * R/pMatrix.R: coercion pMatrix -> Tsparse
259 :    
260 : bates 1300 2006-06-12 Douglas Bates <bates@R-project.org>
261 :    
262 : maechler 1319 * DESCRIPTION (Version): 0.995-11 released to CRAN
263 :    
264 : bates 1300 * R/lmer.R (mcmcsamp method): Corrected arrangments of names on
265 :     the output from mcmcsamp.
266 :    
267 : bates 1298 2006-06-10 Douglas Bates <bates@R-project.org>
268 :    
269 : bates 1300 * R/lmer.R (simulestimate): added C code for calculating the trace
270 :     of the hat matrix.
271 : bates 1298
272 : maechler 1295 2006-06-09 Martin Maechler <maechler@stat.math.ethz.ch>
273 :    
274 :     * R/diagMatrix.R (setAs): define coercion methods to sparse matrix
275 :     classes.
276 : maechler 1315 * R/sparseMatrix.R etc: multiplication of diagonal and sparse
277 : maechler 1295
278 : maechler 1290 2006-06-08 Martin Maechler <maechler@stat.math.ethz.ch>
279 :    
280 :     * R/dgTMatrix.R (colSums): etc. All four of
281 :     colSums(), rowSums(), colMeans(), rowMeans() now should work for
282 :     all "Matrices".
283 :    
284 : bates 1288 2006-06-01 Douglas Bates <bates@stat.wisc.edu>
285 :    
286 :     * R/lmer.R (panel.ci): Add a reference line at zero and a
287 :     background grid to the qqmath plot of ranef.lmer.
288 :    
289 : bates 1287 2006-05-30 Douglas Bates <bates@stat.wisc.edu>
290 : bates 1284
291 : bates 1287 * R/lmer.R (expandSlash): Functions (non-exported) to allow nested
292 :     grouping factors to be specified in the formula as (1|foo/bar).
293 :    
294 :     2006-05-27 Douglas Bates <bates@stat.wisc.edu>
295 :    
296 : bates 1284 * R/lmer.R (findbars and others): Change check of is.numeric to
297 :     !is.language to resolve the bug reported by Jacob Wegelin.
298 :    
299 :     * src/pedigree.c (pedigree_inbreeding): Initial implementation of
300 :     code to evaluate inbreeding coefficients without calculating T,
301 :     based on code in Sargolzaei and Iwaisaki's paper.
302 :    
303 : bates 1283 2006-05-27 Douglas Bates <bates@stat.wisc.edu>
304 :    
305 :     * R/{lmer.R,AllGeneric.R}, src/{init.c,lmer.[ch]}: Added local
306 :     generic and mer methods for isNested and denomDF. This denomDF was
307 :     an attempt to emulate that in lme but I don't think that makes
308 :     sense. Use the trace of the hat matrix instead.
309 :    
310 : maechler 1271 2006-05-17 Martin Maechler <maechler@stat.math.ethz.ch>
311 :    
312 :     * R/sparseMatrix.R: Matrix <-> graph methods: can no longer use
313 :     the C code depending on a slot structure that's no longer valid.
314 : bates 1352 * src/dgTMatrix.c: ditto (also: src/init.c src/dgTMatrix.h)
315 : maechler 1271
316 :    
317 : bates 1268 2006-05-17 Douglas Bates <bates@stat.wisc.edu>
318 :    
319 :     * R/{AllGeneric.R,Csparse.R},man/band.Rd,NAMESPACE: changed name
320 :     of lowerTriMatrix generic and methods to tril (also upper to triu)
321 :     and added a general band extractor.
322 :    
323 : bates 1267 2006-05-16 Douglas Bates <bates@stat.wisc.edu>
324 :    
325 :     * R/pedigree.R (pedigree): Replace sire and dam values outside the
326 :     allowable range with NAs. Added a corresponding check in the
327 :     validity check for the pedigree class.
328 :    
329 :     * R/[CT]sparse.R ([t]crossprod): The result of single-argument
330 :     crossprod methods now inherits from symmetricMatrix.
331 :    
332 : bates 1265 2006-05-15 Douglas Bates <bates@stat.wisc.edu>
333 :    
334 :     * R/AllGeneric.R (lowerTriMatrix): Added (but did not export)
335 :     generics lowerTriMatrix and upperTriMatrix along with methods for
336 :     the Csparse virtual class. Also added a C function Csparse_band
337 :     that implements these methods by calling cholmod_band.
338 :    
339 : maechler 1264 2006-05-15 Martin Maechler <maechler@stat.math.ethz.ch>
340 :    
341 :     * R/Tsparse.R ("["): column or row subsetting; @Dimnames[k] got
342 :     erased when it was NULL. This led to invalid subselections!
343 :    
344 : bates 1259 2006-04-25 Douglas Bates <bates@stat.wisc.edu>
345 :    
346 :     * R/dtCMatrix.R: avoid coercion of dtCMatrix object to dgCMatrix
347 :     in method for "t" so as not to lose the unit diagonal property.
348 :    
349 : bates 1257 2006-04-19 Douglas Bates <bates@stat.wisc.edu>
350 :    
351 :     * R/lmer.R, R/AllGeneric.R, NAMESPACE: Remove the postVar generic
352 :     and methods. This is now an option to the ranef method for the
353 :     mer class.
354 :    
355 :     * src/cs_utils.c: Ensure that the nz component is -1 for a
356 :     compressed column-oriented matrix. Minor formatting cleanup.
357 :    
358 :     * man/lmer-class.Rd: Document the qqmath method for ranef.lmer
359 :     objects.
360 :    
361 : maechler 1253 2006-04-19 Martin Maechler <maechler@stat.math.ethz.ch>
362 :    
363 :     * R/Auxiliaries.R (diagU2N): new for the solve() methods in
364 :     * R/dtCMatrix.R: where dgC -> dgT coercion now preserves diag = "U".
365 :    
366 : bates 1251 2006-04-15 Douglas Bates <bates@stat.wisc.edu>
367 :    
368 :     * src/cs.[ch],src/cs_utils.[ch] : Added Tim Davis' CSparse library
369 :     in cs.[ch] and utilities to interface to that code in cs_utils.[ch].
370 :    
371 :     * R/dtCMatrix.R, src/dtCMatrix.[ch] : CSparse-based solve methods
372 :     for the dtCMatrix class.
373 : maechler 1253
374 : bates 1247 2006-04-12 Douglas Bates <bates@stat.wisc.edu>
375 :    
376 :     * R/pedigree.R, R/AllClass.R, NAMESPACE: added a pedigree class
377 :     and methods for it.
378 :    
379 : maechler 1245 2006-04-12 Martin Maechler <maechler@stat.math.ethz.ch>
380 :    
381 :     * R/dgCMatrix.R: add storage.mode(.) <- "double" for "matrix"
382 :     arguments, such that M %*% 1:6 now works
383 :     * Tests/matprod.R: test the above
384 :    
385 : bates 1244 2006-04-03 Douglas Bates <bates@stat.wisc.edu>
386 : bates 1243
387 :     * R/lmer.R (qqmath,ranef.lmer-method): added a qqmath method for
388 :     the ranef.lmer class.
389 :    
390 :     * R/AllClass.R, NAMESPACE, R/lmer.R: Added a postVar generic and
391 :     methods to extract the posterior variances from the bVar slot.
392 :    
393 : maechler 1238 2006-03-30 Martin Maechler <maechler@stat.math.ethz.ch>
394 :    
395 :     * R/dtCMatrix.R: allow coercion from dgC* to triangular (dtC*)
396 :     * R/dsCMatrix.R: and symmetric (dsC*) 'Csparse' matrices.
397 :    
398 :     * R/Tsparse.R: Tsparse* -> Csparse* coercion now works and is tested in
399 :     * tests/simple: (extended)
400 :    
401 :     * R/sparseMatrix.R (isTriangular): now using much improved
402 :     * R/Auxiliaries.R (isTriC): new triangularity check for *CMatrix
403 :    
404 : bates 1236 2006-03-23 Douglas Bates <bates@stat.wisc.edu>
405 :    
406 :     * src/dsyMatrix.c (dsyMatrix_as_dspMatrix): Propagate DimNames
407 :     (problem report from Franklin Parlamis). This should be done
408 : maechler 1238 generally.
409 : bates 1236
410 : bates 1234 2006-03-21 Douglas Bates <bates@stat.wisc.edu>
411 :    
412 :     * R/AllClass.R,lmer.R: Change the name of the lmer.ranef class to
413 :     ranef.lmer (like summary.lmer). Add the coef.lmer class and
414 :     update the plot methods.
415 :    
416 : bates 1232 2006-03-20 Douglas Bates <bates@stat.wisc.edu>
417 :    
418 :     * R/lmer.R (resid and ranef methods): Added methods for the
419 :     "residuals" and "resid" generic but only for linear mixed model
420 :     fits. Changed the ranef method to return a list of data frames so
421 :     that the plot methods now work.
422 :    
423 : bates 1230 2006-03-16 Douglas Bates <bates@bates2>
424 :    
425 :     * src/dpoMatrix.c (dpoMatrix_chol): Require n > 0 in call to
426 :     dpotrf - otherwise the BLAS on Mac OS X complains and quits.
427 :    
428 :     * DESCRIPTION (Date): New release
429 :    
430 : maechler 1228 2006-03-15 Martin Maechler <maechler@stat.math.ethz.ch>
431 :    
432 :     * DESCRIPTION (Version): 0.995-6 -- to be released to CRAN
433 :    
434 :     * data/KNex.rda: replacing 'mm' and 'y' by KNex <- list(mm=mm, y=y)
435 :     * man/KNex.Rd: and other help files
436 :     * tests/*.R: several ones needed adaption
437 : bates 1352 * inst/doc/Comparisons.Rnw: ditto
438 : maechler 1228
439 : maechler 1226 2006-03-11 Martin Maechler <maechler@stat.math.ethz.ch>
440 :    
441 :     * R/dgCMatrix.R (replCmat): "[<-" methods for dgCMatrix
442 :    
443 :     * tests/indexing.R: tests for new [<- methods for sparse matrices.
444 :    
445 :     2006-03-10 Martin Maechler <maechler@stat.math.ethz.ch>
446 :    
447 :     * R/dgTMatrix.R (replTmat): "[<-" methods for dgTMatrix
448 :    
449 :     * R/Tsparse.R (.ind.prep): fix out-of-range indexing
450 :    
451 :     2006-03-08 Martin Maechler <maechler@stat.math.ethz.ch>
452 :    
453 :     * R/dMatrix.R: enable things like M [ M < 10 ]
454 :     * R/dgeMatrix.R: implement it
455 :    
456 : maechler 1222 2006-03-06 Martin Maechler <maechler@stat.math.ethz.ch>
457 :    
458 :     * R/AllClass.R: define "summary.mer" and "*.lmer"
459 :     * R/lmer.R (summary): summary(<mer>) computes & returns the above;
460 :     * R/lmer.R (show): now works with summary()
461 :    
462 :     2006-03-04 Martin Maechler <maechler@stat.math.ethz.ch>
463 :    
464 :     * R/dgCMatrix.R: finally direct "Arith" dgC o dgC
465 :     * R/Auxiliaries.R (WhichintersectInd): and other utilities to
466 :     support the above
467 :    
468 : bates 1213 2006-02-07 Douglas Bates <bates@stat.wisc.edu>
469 :    
470 :     * R/lmer.R (lmer): fix initial values of offset and weights for glm.fit.
471 :     Use glmFit$prior.weights for weights in a glmm.
472 :     Allow an option usePQL = FALSE to skip the PQL steps for the
473 :     Laplace method (and, in time, the AGQ method).
474 :    
475 :     * src/lmer.c (mer_factor): Move downdating and factoring of XtX
476 :     into a separate function internal_mer_Xfactor to be able to call
477 :     it from internal_bhat.
478 :    
479 : maechler 1200 2006-01-23 Martin Maechler <maechler@stat.math.ethz.ch>
480 :    
481 :     * tests/Class+Meth.R (tstMatrixClass): function for much better
482 :     testing; now again of all actual classes.
483 :    
484 :     * src/Mutils.c (MAKE_TRIANGULAR_BODY, MAKE_SYMMETRIC_BODY):
485 :     use macros and define make_d_matrix_* and make_i_matrix_*
486 :     where _i_ is for the ldense routines:
487 :    
488 :     * src/ldense.c (ltrMatrix_as_lgeMatrix): provide functions
489 :     * src/ldense.c (lsyMatrix_as_lgeMatrix):
490 :    
491 :     * R/ldenseMatrix.R: use the above in setAs(*,"lgeMatrix")
492 :    
493 :    
494 : maechler 1174 2006-01-16 Martin Maechler <maechler@stat.math.ethz.ch>
495 :    
496 :     * R/Matrix.R (Matrix): has become much "smarter" now auto-producing
497 :     many different kinds of matrices.
498 :     * R/*.R: quite a few new methods were needed for R CMD check with
499 :     new Matrix(). Very good for users playing around.
500 :    
501 :    
502 : maechler 1165 2006-01-15 Martin Maechler <maechler@stat.math.ethz.ch>
503 :    
504 :     * src/dgeMatrix.c (dMatrix_validate): new
505 :     * src/Mutils.c (dense_nonpacked_validate): new
506 :    
507 :     * src/dtrMatrix.c (dtrMatrix_validate): improved/fixed
508 :    
509 :    
510 :     2006-01-14 Douglas Bates <bates@stat.wisc.edu>
511 :    
512 :     * R/AllClass.R (compMatrix), (generalMatrix): new virtual classes
513 :    
514 : bates 1123 2006-01-07 Douglas Bates <bates@stat.wisc.edu>
515 : bates 1119
516 : maechler 1127 * DESCRIPTION (Version): 0.99-6 released to CRAN
517 :    
518 : bates 1119 * src/dgBCMatrix.c (cscb_trcbsm): Fix due to Peter Dalgaard for
519 :     segfault in cases with multiple non-nested grouping factors.
520 :    
521 : maechler 1109 2006-01-03 Martin Maechler <maechler@stat.math.ethz.ch>
522 :    
523 :     * DESCRIPTION (Version): 0.99-4 to be released to CRAN
524 :     (Depends): also on 'utils'
525 :    
526 :     * R/AllClass.R (diagonalMatrix): new class with "ddi*" and "ldi*"
527 :     * R/diagMatrix.R (Diagonal): constructor and methods for
528 :     diagonal matrices
529 :    
530 :     * R/ltTMatrix.R: new "minimal methods"
531 :    
532 : maechler 1091 2005-12-12 Martin Maechler <maechler@stat.math.ethz.ch>
533 :    
534 :     * R/AllGeneric.R (tcrossprod): 2-argument version; here, and for
535 :     all methods (and help files).
536 :    
537 : maechler 1084 2005-12-09 Martin Maechler <maechler@stat.math.ethz.ch>
538 :    
539 :     * R/Auxiliaries.R (dimNamesCheck): fixed thinko -> bug
540 :     for case (dimn. op no_dimn.)
541 :    
542 :     2005-11-14 Douglas Bates <bates@stat.wisc.edu>
543 :    
544 : maechler 1174 * DESCRIPTION (Version): 0.99-2 released to CRAN
545 : maechler 1084
546 : bates 988 2005-10-21 Douglas Bates <bates@stat.wisc.edu>
547 :    
548 :     * R/lmer.R (simulate method): Fixed a drop=FALSE problem reported
549 :     by Julian Faraway.
550 :    
551 : maechler 976 2005-10-06 Martin Maechler <maechler@stat.math.ethz.ch>
552 :    
553 :     * R/Auxiliaries.R (try_as): new utility
554 :     * R/sparseMatrix.R: use try_as() in coercion to original class
555 :    
556 : maechler 956 2005-09-30 Martin Maechler <maechler@stat.math.ethz.ch>
557 :    
558 :     * src/dgCMatrix.c (double_to_csc): and dgeMatrix_to_csc()
559 :    
560 :     2005-09-29 Martin Maechler <maechler@stat.math.ethz.ch>
561 :    
562 :     * R/Auxiliaries.R (dimNamesCheck): added
563 :    
564 :     * R/Matrix.R (as.array), (as.vector): new
565 :    
566 : maechler 954 2005-09-28 Martin Maechler <maechler@stat.math.ethz.ch>
567 :    
568 :     * R/Matrix.R (Matrix): get logical argument 'sparse' with a smart
569 : maechler 956 default.
570 :     * R/AllClass.R: move 'factors' slot toplevel "Matrix";
571 :     "pMatrix" now contains "sparseMatrix"
572 : maechler 954
573 : maechler 948 2005-09-26 Martin Maechler <maechler@stat.math.ethz.ch>
574 :    
575 :     * tests/Class+Meth.R: new tests; t(t(m)) == m
576 :    
577 :     * src/dtCMatrix.c (tsc_transpose): add forgotten "diag" slot
578 :    
579 :     * src/dsTMatrix.c (dsTMatrix_as_dsCMatrix): bad typo (segfault!)
580 :     * src/dtTMatrix.c (dtTMatrix_as_dtCMatrix): new
581 :    
582 :     * R/dspMatrix.R: typo in "t" method
583 :    
584 : maechler 925 2005-09-18 Douglas Bates <bates@wisc.edu>
585 :    
586 :     * R/AllClass.R (TsparseMatrix), CsparseM* and RsparseM*
587 :     * R/Tsparse.R: instead of R/gTMatrix.R
588 :     * R/Csparse.R: new
589 :     * src/Tsparse.c (Tsparse_to_Csparse): new; -> cholmod_()
590 :     * src/Tsparse.c: new; many trivial methods calling cholmod_()
591 :     * src/Csparse.c (Csparse_to_Tsparse), transpose, (mat|cross)prod:
592 :     via cholmod
593 :    
594 :     2005-09-16 Martin Maechler <maechler@stat.math.ethz.ch>
595 :    
596 :     * R/Auxiliaries.R (non0ind): new function using new C code
597 :     * src/dgCMatrix.c (compressed_non_0_ij): new utility
598 :    
599 : bates 917 2005-09-15 Douglas Bates <bates@localhost.localdomain>
600 :    
601 :     * src/chm_common.h: header file required by all C sources that
602 : maechler 1174 call CHOLMOD functions. It defines a cholmod_common structure
603 : bates 917 called 'c' whose address is passed as the last argument to
604 :     (virtually) every CHOLMOD function.
605 :    
606 :     * src/Pattern.c: Simple example of the use of CHOLMOD.
607 :    
608 :     * src/init.c: initialize and finalize the cholmod_common structure.
609 :    
610 :     * src/Makefile: Added source packages CHOLMOD UMFPACK AMD COLAMD
611 :     LDL and CCOLAMD from the U. of Florida sparse matrix library.
612 :    
613 : maechler 908 2005-09-08 Martin Maechler <maechler@stat.math.ethz.ch>
614 :    
615 :     * inst/test-tools.R: new file collecting the utility functions used
616 :     in ./tests/*.R
617 :    
618 :     * R/ddenseMatrix.R (cbind2): new methods for "numeric" and "matrix"
619 :     * R/Matrix.R (cbind2): methods for NULL and missing
620 :    
621 : maechler 886 2005-08-31 Martin Maechler <maechler@stat.math.ethz.ch>
622 :    
623 :     * R/AllClass.R: new "index" class for "[" and "[<-":
624 :     First cut at "symmetricMatrix" and "triangularMatrix"
625 :     * R/gTMatrix.R (.ind.prep): new function;
626 : maechler 1174 Logical and character indexing now work too.
627 : maechler 886 * R/Matrix.R: cheap "[<-" methods for denseMatrix now work
628 :     * tests/indexing.R: new, including *.Rout.save
629 :     * tests/dgTMatrix.R: new
630 :    
631 : bates 876 2005-08-29 Douglas Bates <bates@wisc.edu>
632 :    
633 :     * src/dgTMatrix.c (graphNEL_as_dgTMatrix): Corrected the position
634 :     indicator pos not being updated. Also enforced upper triangular
635 :     for symmetric case. Need to coerce edges component of elements of
636 :     edge list - grr! (Why don't they define their classes cleanly?)
637 :    
638 : maechler 871 2005-08-26 Martin Maechler <maechler@stat.math.ethz.ch>
639 :    
640 :     * R/Matrix.R: added first "[<-" methods; not yet functional
641 : bates 1352 * R/denseMatrix.R: ditto
642 : maechler 871 * man/Subassign-methods.Rd: new help file for these
643 :    
644 :     2005-08-25 Martin Maechler <maechler@stat.math.ethz.ch>
645 :    
646 :     * DESCRIPTION (Version): 0.98-6
647 :    
648 :     * R/denseMatrix.R: new file for "[" fallback methods for all dense
649 :     matrices.
650 :    
651 : maechler 868 2005-08-19 Martin Maechler <maechler@stat.math.ethz.ch>
652 :    
653 :     * src/lgCMatrix.c (lcsc_to_matrix): new; need for
654 :     as( <logical>, "matrix")
655 :    
656 :     * R/pMatrix.R: coercion to "lgTMatrix"
657 :    
658 :     * R/gTMatrix.R: new virtual class to define "[" methods for.
659 :     * man/gTMatrix-class.Rd:
660 :     * General slight re-organization of where "[" methods are defined.
661 :     more to come.
662 :    
663 : maechler 871 2005-08-18 Douglas Bates <bates@wisc.edu>
664 : maechler 868
665 : maechler 1174 * DESCRIPTION (Version): 0.98-5 released to CRAN
666 : maechler 871
667 :     * src/dgTMatrix.c (graphNEL_as_dgTMatrix): add first graphNEL methods
668 :     * .....
669 :    
670 : bates 863 2005-08-18 Douglas Bates <bates@localhost.localdomain>
671 :    
672 :     * R/lmer.R: Corrected naming scheme in mcmcsamp to work with lmer
673 :     or glmer objects.
674 :    
675 : maechler 860 2005-08-17 Martin Maechler <maechler@stat.math.ethz.ch>
676 :    
677 :     * DESCRIPTION (Version): 0.98-4 : upload to CRAN
678 :    
679 :     2005-08-16 Douglas Bates <bates@localhost.localdomain>
680 :    
681 :     * R/HBMM.R: finish re-writing R-only code.
682 :    
683 : bates 854 2005-08-15 Douglas Bates <bates@localhost.localdomain>
684 :    
685 :     * man/externalFormats.Rd: move documentation for writeHB and
686 :     writeMM here.
687 :    
688 :     * src/mmio.c: replace inclusion of <malloc.h> by <stdlib.h>
689 :     (suggested by Paul Roecker).
690 :    
691 :     * tests/validObj.R (assertError): Comment out test that is failing
692 :     after recent changes in r-devel.
693 :    
694 : maechler 860
695 : maechler 848 2005-08-11 Martin Maechler <maechler@stat.math.ethz.ch>
696 :    
697 :     * R/AllClass.R: intermediate virtual class "denseMatrix"
698 :     * man/denseMatrix-class.Rd
699 :     * NAMESPACE: export it, and also export
700 :     * man/unused-classes.Rd: "iMatrix", "zMatrix" and "ldenseMatrix"
701 :    
702 : bates 846 2005-08-10 Douglas Bates <bates@wisc.edu>
703 :    
704 : maechler 848 * DESCRIPTION (Version): 0.98-3 to CRAN
705 :    
706 : bates 846 * src/dtrMatrix.c (dtrMatrix_validate): fixed up validation and
707 :     matrix_solve code (which was really, really wrong).
708 :    
709 : bates 835 2005-08-07 Douglas Bates <bates@wisc.edu>
710 : maechler 834
711 :     * DESCRIPTION (Version): 0.98-2
712 :    
713 :     * R/HBMM.R (readHB), (readMM): read Matrix Market formats
714 :    
715 :     * R/lmer.R (abbrvNms): new
716 :     * R/lmer.R (mcmcsamp): allow transformed parameters
717 : bates 835 * src/HBMM.c (Matrix_writeMatrixMarket): Added read/write routines
718 :     for the Harwell-Boeing and the MatrixMarket formats.
719 : maechler 834
720 :     2005-08-04 Martin Maechler <maechler@stat.math.ethz.ch>
721 :    
722 :     * man/dtrMatrix-class.Rd: add examples
723 : bates 835 * man/dtpMatrix-class.Rd: ditto; plus note about PROBLEM
724 : maechler 834
725 :     * TODO: note the dtpMatrix (docu) bug
726 :    
727 :     * R/zzz.R (.onLoad): assignInNamespace("as.matrix", *, "base")
728 :     in order to ensure that new as.matrix() is used by old functions,
729 :     e.g., svd(), qr(), eigen(), dist(),..;
730 :     apply(), also matplot() or pairs().
731 :    
732 :    
733 :     2005-08-03 Martin Maechler <maechler@stat.math.ethz.ch>
734 :    
735 :     * R/lmer.R: add 'fixme' comments and move the linear vs glm check;
736 :     add comments about 'control' / lmerControl() arguments
737 :    
738 : bates 835 2005-07-27 Douglas Bates <bates@wisc.edu>
739 : bates 820
740 : bates 835 * man/sleepstudy.Rd: Added the sleep data set.
741 : maechler 1174 * DESCRIPTION (Version): 0.98-1 released to CRAN
742 : bates 820
743 : bates 835 2005-07-12 Douglas Bates <bates@wisc.edu>
744 : maechler 834 * man/sleepstudy.Rd: Added the sleep data set.
745 :    
746 : bates 809 * R/lmer.R (glmmMCMC): Added PACKAGE = "Matrix" in a couple of
747 :     .Call calls that were producing spurious output.
748 :    
749 : bates 835 2005-07-05 Douglas Bates <bates@wisc.edu>
750 : bates 801
751 :     * R/lmer.R (lmer): stored updated variance component estimates in
752 :     mer object for the generalized model. (Bug reported by Renaud
753 :     Lancelot).
754 :    
755 : bates 835 2005-07-03 Douglas Bates <bates@wisc.edu>
756 : bates 794
757 :     * src/lmer.c (glmer_devAGQ): Added AGQ for single grouping factor,
758 :     unidimensional case.
759 :    
760 : bates 835 2005-06-08 Douglas Bates <bates@wisc.edu>
761 : maechler 791
762 :     * DESCRIPTION (Version): 0.96-1
763 :    
764 : maechler 1174 * moved lmer-class' R and C code moved from lme4 to here
765 : maechler 791
766 : bates 835 2005-06-04 Douglas Bates <bates@wisc.edu>
767 : bates 763
768 :     * R/dgCMatrix.R: Call to csc_matrix_mm used undefined arguments
769 :     (reported by Guissepe Ragusa <gragusa@ucsd.edu>)
770 :    
771 : bates 835 2005-06-02 Douglas Bates <bates@wisc.edu>
772 : bates 763
773 :     * src/Makefile.win: Forgot to update this when Makefile changed.
774 :    
775 : bates 835 2005-05-11 Douglas Bates <bates@wisc.edu>
776 : bates 726
777 :     * src/dgCMatrix.c (csc_transpose): Simplified function fixing a
778 :     bug reported by Kurt Hornik and Michael Hahsler.
779 :    
780 : bates 835 2005-05-10 Douglas Bates <bates@wisc.edu>
781 : bates 725
782 :     * src/lgCMatrix.c (Matrix_lgClgCmm): Implementation of methods for
783 :     logical sparse matrices. These will also be used in the symbolic
784 :     analysis for lmer objects.
785 :    
786 :     * src/dsCMatrix.c (dsCMatrix_matrix_solve): Copied the dimensions
787 :     of b to the result. Fixes bug reported by Jean.Coursol@math.u-psud.fr
788 : maechler 791
789 : bates 835 2005-05-06 Douglas Bates <bates@wisc.edu>
790 : bates 714
791 :     * src/dgeMatrix.c (dgeMatrix_colsums): Added an implementation of
792 :     colMeans, colSums, rowMeans and rowSums.
793 :    
794 : bates 835 2005-04-18 Douglas Bates <bates@wisc.edu>
795 : bates 692
796 :     * src/lgCMatrix.[ch]: code for _validate method and stub for
797 :     multiplication operation.
798 :    
799 :     * src/dgeMatrix.c (dgeMatrix_matrix_solve): Passing wrong argument
800 :     to dgetrs.
801 :    
802 :     * src/init.c: Fix cut-and-paste error in definition of
803 :     dgeMatrix_matrix_solve
804 :    
805 :     * src/{many files}: Tighten code by using ALLOC_SLOT.
806 :    
807 : bates 835 2005-04-15 Douglas Bates <bates@wisc.edu>
808 : bates 692
809 :     * R/AllClass.R: Add lgTMatrix and lgCMatrix classes
810 :    
811 :     * DESCRIPTION: Eliminate import of stats.
812 :    
813 : maechler 791
814 : bates 835 2005-04-06 Douglas Bates <bates@wisc.edu>
815 : bates 692
816 :     * R/AllClass.R : add logical sparse matrix classes
817 :    
818 : maechler 687 2005-04-01 Martin Maechler <maechler@stat.math.ethz.ch>
819 :    
820 :     * R/dgTMatrix.R: add "[" method for triplet matrices
821 :     * R/sparseMatrix.R: and other sparse ones; --> add show() for sparse
822 :    
823 : bates 835 2005-03-31 Douglas Bates <bates@wisc.edu>
824 : maechler 687
825 :     * DESCRIPTION (Version): release 0.95-5 to CRAN
826 :    
827 :     * R/dMatrix.R: add %*%, crossprod and solve "fallback" methods
828 :     * R/sparseMatrix.R: %*%, crossprod()
829 :     * R/dgeMatrix.R: more "fallback" methods for numeric/dense matrices
830 :     * man/*.Rd: move method definitions to 'Matrix' and 'dMatrix'
831 :     * src/lmer.c (lmer_fitted): fix thinko
832 :    
833 : maechler 676 2005-03-26 Martin Maechler <maechler@stat.math.ethz.ch>
834 :    
835 :     * R/AllClass.R: add two virtual sparse classes ``on top''
836 :    
837 :     2005-03-24 Martin Maechler <maechler@stat.math.ethz.ch>
838 :    
839 :     * R/AllClass.R (setClass): use "VIRTUAL" for the virtual classes;
840 :     correspondingly fix examples and tests/ since new()
841 :     doesn't work for virtual classes.
842 :    
843 : maechler 658 2005-03-17 Martin Maechler <maechler@stat.math.ethz.ch>
844 :    
845 :     * R/Matrix.R (as.matrix): method and one for unname()
846 :     * tests/dpoMatrix.R: tests should now be less platform dependent;
847 :     also run for R 2.1.0; using as.matrix()
848 :    
849 : bates 835 2005-03-15 Douglas Bates <bates@wisc.edu>
850 : maechler 658
851 :     * R/pMatrix.R: "pMatrix" class added
852 :     * ....
853 :    
854 : bates 835 2005-03-14 Douglas Bates <bates@wisc.edu>
855 : bates 645
856 :     * R/dtpMatrix.R: Add unpack method and an example.
857 :    
858 :     * src/dsyMatrix.c (dsyMatrix_trf): Add BunchKaufman factorization
859 :     of general symmetric matrices and associated S4 methods.
860 :    
861 : maechler 658 2005-03-10 Martin Maechler <maechler@stat.math.ethz.ch>
862 :     +
863 :     2005-03-05 Martin Maechler <maechler@stat.math.ethz.ch>
864 :    
865 :     * R/dgeMatrix.R (setAs): and many other files: more coercion,
866 :     crossprod() and "%*%" methods added; tests, too.
867 :     * tests/matprod.R: new, for testing these
868 :    
869 : bates 835 2005-03-03 Douglas Bates <bates@wisc.edu>
870 : bates 599
871 :     * src/lmer.c (lmer_fitted): Added.
872 :    
873 : bates 835 2005-03-02 Douglas Bates <bates@wisc.edu>
874 : bates 596
875 :     * R/dsTMatrix.R: Conversion from dsTMatrix to dsCMatrix
876 :    
877 : bates 835 2005-02-28 Douglas Bates <bates@wisc.edu>
878 : bates 582
879 :     * src/*.c,po/,inst/po: Internationalization and localization of
880 :     the package.
881 :    
882 :     * src/ldl.[ch]: Removed these as their contents are referenced in the
883 :     R_ldl.c file.
884 :    
885 :     * src/flame.[ch]: Removed these source files.
886 : maechler 658
887 : bates 582 * src/dtrMatrix.c (make_array_triangular): Move to Mutils
888 :    
889 :     * src/LU.[ch],src/init.c: absorb in factorizations
890 :    
891 :     * src/Mutils.h: prepare for internationalization
892 :    
893 :     * src/cblas.h: move the enum definitions to Mutils.h and remove
894 :     this file
895 :    
896 : maechler 578 2005-02-26 Martin Maechler <maechler@stat.math.ethz.ch>
897 :    
898 : maechler 579 * R/dgeMatrix.R: provide "dimnames" and "dimnames<-" methods
899 :    
900 :     * R/dtrMatrix.R: fix t() method
901 :    
902 : maechler 578 * R/dgeMatrix.R: define group methods "Arith", "Math", "Math2"
903 : maechler 658 * NAMESPACE: export them (and import generics from "methods")
904 : maechler 578 * tests/group-methods.R : and test them.
905 :    
906 :     * src/dtrMatrix.c (dtrMatrix_as_dgeMatrix): prevent seg.fault in
907 :     border case
908 :    
909 :     2005-02-24 Douglas Bates <bates@stat.wisc.edu>
910 :    
911 : maechler 658 * DESCRIPTION (Version): 0.95-2 released to CRAN
912 : maechler 578
913 :     * src/dgBCMatrix.c:
914 :     * src/lmer.c: many changes
915 :     * ...
916 :    
917 : maechler 512 2005-02-04 Martin Maechler <maechler@stat.math.ethz.ch>
918 :    
919 :     * R/Matrix.R: add more sophisticated show() method.
920 :    
921 : maechler 578 2005-02-02 Douglas Bates <bates@stat.wisc.edu>
922 :    
923 :     * */* : almost complete reorganization of classes.
924 :    
925 : bates 835 2005-01-26 Douglas Bates <bates@wisc.edu>
926 : bates 460
927 :     * R/AllGeneric.R: Added matrix exponential generic expm and a method
928 :     for the geMatrix class.
929 :    
930 : bates 835 2005-01-24 Douglas Bates <bates@wisc.edu>
931 : bates 460
932 :     * src/Makefile (clean): Remove *.a and *.so
933 :    
934 :     * man/cscBlocked-class.Rd: Remove reference to the lmer-class.
935 :    
936 : bates 835 2005-01-23 Douglas Bates <bates@wisc.edu>
937 : bates 460
938 : maechler 658 * src/lmer.c (Lind): Definition of Lind was backwards. This only
939 : bates 460 had an effect in cases with more than 2 grouping factors.
940 :    
941 : bates 835 2005-01-03 Douglas Bates <bates@wisc.edu>
942 : bates 415
943 :     * src/lmeRep.c (lmer_variances): change from lmeRep to lmer
944 :    
945 : bates 835 2004-12-23 Douglas Bates <bates@wisc.edu>
946 : bates 410
947 :     * src/init.c (R_init_Matrix): Reorder calls to R_registerRoutines
948 :     and R_useDynamicSymbols (suggested by B.D.Ripley).
949 :    
950 : bates 835 2004-12-14 Douglas Bates <bates@wisc.edu>
951 : bates 392
952 :     * R/sscMatrix.R: Add determinant methods
953 :    
954 :     * src/triplet.[ch],src/init.c (triplet_to_matrix): Add a coercion
955 :     for tripletMatrix to matrix.
956 :    
957 : bates 835 2004-12-13 Douglas Bates <bates@wisc.edu>
958 : bates 388
959 : bates 392 * R/AllClass.R (.onLoad): Eliminate the bbCrosstab class, which is
960 :     no longer used.
961 :    
962 : bates 388 * src/R_ldl.c: Created an R-specific version of the ldl.[ch] files
963 :     with dynamic allocation of scratch arrays.
964 :    
965 :     * src/ssclme.c (ssclme_copy_ctab): Fixed bug in creation of ZtZ
966 :     for multivariate random effects with multiple grouping factors.
967 :     Fixes part but not all of #15.
968 :    
969 : bates 835 2004-12-03 Douglas Bates <bates@wisc.edu>
970 : bates 375
971 :     * src/lmeRep.c (lmeRep_factor): order of operations for multiple
972 :     scalar grouping factors corrected.
973 :    
974 : bates 835 2004-11-29 Douglas Bates <bates@wisc.edu>
975 : bates 375
976 :     * src/bCrosstab.c: remove diag_update which is no longer used
977 :    
978 : bates 835 2004-11-16 Douglas Bates <bates@wisc.edu>
979 : bates 350
980 :     * src/Metis_utils.c: Move metis.h include to C sources so that the
981 :     .h file can be included.
982 :    
983 : bates 835 2004-11-12 Douglas Bates <bates@wisc.edu>
984 : bates 342
985 : bates 350 * src/LU.c,geMatrix.c,trMatrix.c, etc.:
986 : bates 342 Complete allocation of slots in NEW_OBJECT.
987 :    
988 :     * src/Mutils.h: Moved list of symbols to an include file
989 :    
990 : bates 835 2004-11-11 Douglas Bates <bates@wisc.edu>
991 : bates 342
992 :     * src/geMutils.c (Matrix_init): remove unused function
993 :    
994 : bates 835 2004-11-10 Douglas Bates <bates@wisc.edu>
995 : bates 342
996 :     * src/cscMatrix.c (csc_to_imagemat): removed unused function
997 :    
998 : bates 835 2004-11-05 Douglas Bates <bates@wisc.edu>
999 : bates 327
1000 :     * src/Makefile.win (SOURCES_C): Keep consistent with Makefile
1001 :    
1002 : bates 835 2004-10-27 Douglas Bates <bates@wisc.edu>
1003 : bates 303
1004 :     * R/pdmatrix.R: remove PACKAGE="Matrix" in .Call calls
1005 :    
1006 : bates 835 2004-10-04 Douglas Bates <bates@wisc.edu>
1007 : bates 296
1008 :     * src/init.c: Created R_init_Matrix and added registration of C
1009 :     routines.
1010 :    
1011 : bates 835 2004-10-02 Douglas Bates <bates@wisc.edu>
1012 : bates 283
1013 :     * R/tripletMatrix.R: Force a require(lattice) for the image methods.
1014 :    
1015 : bates 835 2004-06-15 Douglas Bates <bates@wisc.edu>
1016 : bates 229
1017 :     * man/trMatrix-class.Rd: Escape the % chars in .Rd files.
1018 :    
1019 : bates 111 2004-04-20 Douglas Bates <bates@stat.wisc.edu>
1020 :    
1021 :     * src/Makefile.win ($(SHLIB)): Modifications per Uwe Ligges.
1022 :    
1023 : bates 109 2004-04-19 Douglas Bates <bates@stat.wisc.edu>
1024 :    
1025 :     * src/ssclme.c (ssclme_update_mm): fix logic error in
1026 :     ssclme_update_mm
1027 :    
1028 : bates 105 2004-04-18 Douglas Bates <bates@stat.wisc.edu>
1029 :    
1030 :     * src/ssclme.c (ssclme_coef, ssclme_coefGets): Create consistency
1031 :     in the order of unconstrained and constrained parameters.
1032 :     (ssclme_gradient): Added the gradients (not yet correct for
1033 :     multidimensional, unconstrained case).
1034 :    
1035 : bates 78 2004-04-14 Douglas Bates <bates@stat.wisc.edu>
1036 :    
1037 :     * src/ssclme.c (ssclme_EMsteps): Fix logic in REML update
1038 :    
1039 :     * src/Makefile.win: Remove unneeded ranlib call
1040 :    
1041 : bates 71 2004-04-12 Douglas Bates <bates@stat.wisc.edu>
1042 :    
1043 :     * DESCRIPTION (Version): New release
1044 :    
1045 :     * src/Makefile.win: Update Makefile.win to umfpack removal.
1046 :    
1047 : bates 49 2004-04-05 Douglas Bates <bates@bates2_home>
1048 :    
1049 :     * src/triplet_to_col.c: Create triplet_to_col as a native
1050 : maechler 658 function, not the version from umfpack. There were problems with
1051 : bates 49 the configuration of UMFPACK for 64-bit processors and there was
1052 :     only one umfpack routine being used so I moved it here.
1053 :    
1054 : bates 45 2004-04-04 Douglas Bates <bates@bates2_home>
1055 :    
1056 :     * src/ssclme.c (ssclme_variances): New function.
1057 :    
1058 : bates 28 2004-03-28 Douglas Bates <bates@bates2_home>
1059 :    
1060 :     * src/ssclme.c (ssclme_fitted): Added function.
1061 :    
1062 : bates 22 2004-03-27 Douglas Bates <bates@bates2_home>
1063 :    
1064 :     * src/ssclme.c (ssclme_transfer_dimnames): Add new function to
1065 :     store the dimnames in the XtX and bVar slots
1066 :     (ssclme_update_mm): Change the dimensions of the bVar slot
1067 :     components and the returned value from ssclme_ranef.
1068 :    
1069 : bates 10 2004-03-18 Douglas Bates <bates@stat.wisc.edu>
1070 :    
1071 :     * R/{pdMat.R,pdIdent.R,pdLogChol.R,pdMatrixLog.R,pdNatural.R},
1072 :     src/{pdMat.c,pdIdent.c,pdLogChol.c,pdNatural.c},
1073 :     tests/{pdCompSymm.R,pdDiag.R,pdIdent.R,pdLogChol.R,pdNatural.R},
1074 :     man/{pdMat-class.Rd,pdmatrix-class.Rd,corrmatrix-class.Rd,
1075 :     pdDiag-class.Rd,pdIdent-class.Rd,pdNatural-class.Rd,
1076 :     pdLogChol-class.Rd,coefGets.Rd,pdCompSymm-class.Rd,
1077 :     pdfactor-class.Rd,pdFactor.Rd,pdMatrix.Rd,
1078 :     pdBlocked-class.Rd},AllClass.R,AllGeneric.R:
1079 :     Moved the pdMat classes from the lme4 package.
1080 :    
1081 :     2004-03-02 Douglas Bates <bates@stat.wisc.edu>
1082 :    
1083 :     * man/ssclme-class.Rd: Update definition and documentation of the
1084 :     ssclme class to include the DIsqrt slot.
1085 :    
1086 :     * src/ssclme.c (ssclme_deviance): Modify order of computation
1087 :     (much faster using dsyrk, a level 3 BLAS routine).
1088 :    
1089 :     * src/Makefile (SUBLIBS): Change definition (K. Hornik)
1090 :    
1091 :     2004-02-28 Douglas Bates <bates@stat.wisc.edu>
1092 :    
1093 :     * tests/ssclme.R: Modify the test to account for the permutation
1094 :     of the levels of the grouping factors.
1095 :    
1096 :     2004-02-23 Douglas Bates <bates@stat.wisc.edu>
1097 :    
1098 :     * R/ssclme.R,src/ssclme.c (ssclme): Move slots of sscCrosstab slot
1099 :     directly into the ssclme class definition.
1100 :    
1101 :     2004-02-22 Douglas Bates <bates@stat.wisc.edu>
1102 :    
1103 :     * DESCRIPTION (Date): New release
1104 :    
1105 :     * man/ssclme-class.Rd: new file.
1106 :    
1107 :     * src/ssclme.c (ssclme_loglik): major revisions in design. It
1108 :     works and it's fast!
1109 :    
1110 :     2004-02-17 Douglas Bates <bates@stat.wisc.edu>
1111 :    
1112 :     * src/taucs/Makefile.win (lib): Change "ar" to "$(AR)" (B.Ripley)
1113 :    
1114 :     2004-02-16 Douglas Bates <bates@stat.wisc.edu>
1115 :    
1116 :     * DESCRIPTION (Date): New release
1117 :    
1118 :     * NAMESPACE: Don't export ssclme.
1119 :    
1120 :     * data/ScotsSec.rda, man/ScotsSec.Rd: Add Scottish secondary
1121 :     school data.
1122 :    
1123 :     2004-02-11 Douglas Bates <bates@stat.wisc.edu>
1124 :    
1125 :     * src/sscCrosstab.c (sscCrosstab): Added a row to the incidence to
1126 :     keep track of the fixed-effects and the response. Counts also
1127 :     gets an extra element, which is always one.
1128 :    
1129 :     * src/ldl.c: Include these routines from Tim Davis' LDL package.
1130 :    
1131 :     2004-02-10 Douglas Bates <bates@stat.wisc.edu>
1132 :    
1133 :     * src/cscMatrix.c (csc_transpose): new function
1134 :    
1135 :     * src/Mutils.c (csc_sort_columns): perm/iperm confusion corrected
1136 :     (csc_components_transpose): new function
1137 :    
1138 :     2004-02-06 Douglas Bates <bates@stat.wisc.edu>
1139 :    
1140 :     * src/triplet.c (triplet_validate): Fix Dim slot on generated
1141 :     triplets
1142 :    
1143 :     2004-01-30 Douglas Bates <bates@stat.wisc.edu>
1144 :    
1145 :     * R/sscCrosstab.R (sscCrosstab): Added sscCrosstab generator function.
1146 :    
1147 :     * src/LU.h (MATRIX_LU_H): Add #ifndef #define ... #endif to this
1148 :     and all other .h files in src.
1149 :    
1150 :     * src/Makefile.win: This and other Makefile.win files contributed
1151 :     by Brian Ripley.
1152 :    
1153 :     2004-01-27 Douglas Bates <bates@stat.wisc.edu>
1154 :    
1155 :     * R/syMatrix.R: Added methods for "%*%".
1156 :    
1157 :     * R/Hilbert.R (Hilbert): Changed Hilbert function to return a
1158 :     poMatrix object.
1159 :    
1160 :     2004-01-26 Douglas Bates <bates@stat.wisc.edu>
1161 :    
1162 :     * man/sscChol-class.Rd,man/mm.Rd,man/y.Rd: Added man pages.
1163 :    
1164 :     2004-01-25 Douglas Bates <bates@bates2_home>
1165 :    
1166 :     * inst/doc/Introduction.Rnw,Comparisons.Rnw: Added vignettes.
1167 :    
1168 :     * R/csc.R: Convert all cscMatrix classes to use Dim slot instead
1169 :     of nrow.
1170 :    
1171 :     2003-12-31 Douglas Bates <bates@stat.wisc.edu>
1172 :    
1173 :     * src/taucs/taucs.h: Moved taucs.h, amd.h, and umfpack.h into
1174 :     subdirectories.
1175 :    
1176 :     2003-12-08 Douglas Bates <bates@stat.wisc.edu>
1177 :    
1178 :     * src/taucs.h: Accidently referred to global header files
1179 :     instead of local files.
1180 :    
1181 :     2003-12-04 Douglas Bates <bates@stat.wisc.edu>
1182 :    
1183 :     * R/AllClass.R: Lots of changes. Removed all the lapack++ code
1184 :     and methods and replaced all classes with S4 classes.
1185 :    
1186 :     2003-04-19 Douglas Bates <bates@stat.wisc.edu>
1187 :    
1188 :     * R/det.R,man/det.Rd: Change name of det generic to determinant
1189 :    
1190 :     * src/R_LapackPP.cc: Change method of calculating determinants
1191 :    
1192 :     2003-02-03 Douglas Bates <bates@stat.wisc.edu>
1193 :    
1194 :     * DESCRIPTION (Version): removed empty data directory as requested
1195 :     by CRAN maintainers. Changed version number and date.
1196 :    
1197 :     2002-10-23 Douglas Bates <bates@stat.wisc.edu>
1198 :    
1199 :     * src/laindex.h: Applied patches from Brian Ripley for compilation
1200 :     under Windows.
1201 :    
1202 :     * Added configure.win and src/Makevars.win as requested by Brian
1203 :     Ripley.
1204 :    
1205 :     2002-05-03 Douglas Bates <bates@stat.wisc.edu>
1206 :    
1207 :     * src/lamatrix.h: Removing pre-1.2.0 compatibility code per Kurt
1208 :     Hornik.
1209 :    
1210 :     2002-04-24 Douglas Bates <bates@stat.wisc.edu>
1211 :    
1212 :     * configure.ac: Replaced configure.in with configure.ac
1213 :     contributed by Kurt Hornik.
1214 :    
1215 :     * aclocal.m4 (ac_clean_files): Replaced this with Kurt Hornik's
1216 :     version for R-1.5.0
1217 :    
1218 : maechler 512
1219 : bates 10 2001-12-10 Douglas Bates <bates@stat.wisc.edu>
1220 :    
1221 :     * man/eigen.Rd: Removed the .Alias in the example

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