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Annotation of /pkg/ChangeLog

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Revision 1411 - (view) (download)

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 : bates 1411 * tests/matprod.R: Add tests to verify that 'solve' and '%*%' are
6 :     inverses.
7 :     * src/sparseQR.c (sparseQR_validate): add new validation test, fix
8 :     -Wall warnings.
9 :     * src/dppMatrix.c,dtrMatrix.c,dgCMatrix.c,dgeMatrix.c,dspMatrix.c:
10 :     Use dup_mMatrix_as_dgeMatrix.
11 :    
12 : bates 1403 2006-08-20 Douglas Bates <bates@R-project.org>
13 :    
14 :     * src/sparseQR.c: Fix thinko in sparseQR_resid_fitted.
15 :     * tests/sparseQR.R: Added
16 :     * man/sparseQR-class.Rd: Document methods for qr.* generics
17 :     * R/sparseQR.R: Return correct # of coefs; fix cut-and-paste errors
18 :    
19 : bates 1398 2006-08-19 Douglas Bates <bates@R-project.org>
20 :    
21 :     * NAMESPACE, R/sparseQR.R, src/init.c,sparseQR.[ch],SOURCES_C.mkf:
22 :     Added methods for sparseQR for qr.qy, qr.qty, qr.coef, qr.resid
23 :     and qr.fitted.
24 :     * src/Mutils.[ch]: Added dup_mMatrix_as_dgeMatrix utility
25 :     * src/dgCMatrix.c: Check for ordering before storing q in dgCMatrix_QR
26 :    
27 : maechler 1389 2006-08-18 Martin Maechler <maechler@stat.math.ethz.ch>
28 :    
29 :     * R/AllGeneric.R: add "qr" and "chol" generics; via 'trick' since
30 :     the base version has no "..." argument.
31 :    
32 :     * R/sparseMatrix.R (prSpMatrix): fix the triangular unit diagonal case.
33 :    
34 :     * R/Matrix.R: define and
35 :     * NAMESPACE: export as.numeric() and as.logical() methods.
36 :     Let's hope these do not badly slow down something...
37 :     Finally export the zapsmall() method.
38 :    
39 : bates 1388 2006-08-17 Douglas Bates <bates@R-project.org>
40 :    
41 :     * src/dgCMatrix.[ch] (dgCMatrix_matrix_solve), src/init.c,
42 :     R/dgCMatrix.R: solve methods for dgCMatrix and dense RHS.
43 :     * src/dtCMatrix.c :Remove code that is no longer used
44 :     * R/dtCMatrix.R: Use C code for diagU2N in CsparseMatrix classes
45 :    
46 : bates 1370 2006-08-14 Douglas Bates <bates@R-project.org>
47 :    
48 : bates 1373 * src/Csparse.[ch],init.c (Csparse_to_logical): Added utilities
49 :     Csparse_to_logical and Csparse_symmetric_to_general.
50 :     * R/dgCMatrix.R,dsCMatrix.R,Csparse.R : Consolidate general
51 : maechler 1389 coercion methods between CsparseMatrix and TsparseMatrix.
52 : bates 1373
53 :     2006-08-14 Douglas Bates <bates@R-project.org>
54 :    
55 : bates 1370 * R/dtCMatrix.R,dgCMatrix.R,Csparse.R src/init.c,dgCMatrix.[ch],
56 :     Csparse.[ch],chm_common.c,dense.c : Use CHOLMOD code and methods
57 :     for CsparseMatrix, TsparseMatrix, denseMatrix or matrix when
58 :     possible.
59 :    
60 : bates 1368 2006-08-12 Douglas Bates <bates@R-project.org>
61 :    
62 :     * src/chm_common.[ch],Csparse.[ch],Tsparse.[ch],CHMfactor.c,dtTMatrix.c,
63 :     dgTMatrix.c,dgCMatrix.c,dsCMatrix.c,dtTMatrix.c, R/dsTMatrix.R,
64 :     Tsparse.R,Csparse.R,dgTMatrix.R,dsCMatrix.R,lsCMatrix.R:
65 :     generalize conversions between TsparseMatrix, CsparseMatrix,
66 :     denseMatrix and matrix. Preserve triangularity property and
67 :     propagate Dimnames in the easy cases.
68 :    
69 : bates 1365 2006-08-10 Douglas Bates <bates@R-project.org>
70 :    
71 :     * src/lmer.c: adjust checks in glmer_init for S4SXP
72 :     * tests/validObj.R: check of all(eq) should be all(eq@x) - worked
73 :     before S4SXP but for the wrong reasons.
74 :    
75 : bates 1354 2006-08-08 Douglas Bates <bates@R-project.org>
76 :    
77 : bates 1360 * src/Csparse.c (Csparse_crossprod): tcrossprod result has stype = -1.
78 :     Later modified to return the upper triangle only.
79 :     * R/dgTMatrix.R: Remove vestigial crossprod and tcrossprod methods.
80 : maechler 1389
81 : bates 1352 2006-08-07 Douglas Bates <bates@R-project.org>
82 :    
83 :     * src/Csparse.c (Csparse_crossprod): Set stype on result to avoid
84 :     R-level conversion to a sparse symmetric class.
85 :     * R/Tsparse.R,R/Csparse.R (crossprod and tcrossprod methods):
86 :     Remove conversion to sparse symmetric classes (now done in C code).
87 :    
88 : maechler 1349 2006-08-07 Martin Maechler <maechler@stat.math.ethz.ch>
89 :    
90 : maechler 1351 * R/dgCMatrix.R: disable old crossprod and tcrossprod methods
91 :     * man/band.Rd: adapt the \dontshow{} unit test.
92 :    
93 :     2006-08-07 Martin Maechler <maechler@stat.math.ethz.ch>
94 :    
95 : maechler 1349 * DESCRIPTION (Version): 0.995-14 for CRAN
96 :    
97 :     * tests/other-pkgs.R: oops: library(Matrix) outside *if* !
98 :    
99 :     * R/sparseMatrix.R (Tsp2grNEL): fixed Tsparse -> graph coercion
100 :     * tests/other-pkgs.R: more checks, sparseMatrix -> graph
101 :    
102 :     * R/Auxiliaries.R (as_Tsparse, as_Rsparse): new
103 :     * R/Tsparse.R (tril, triu, band): methods
104 : bates 1352 * R/dgRMatrix.R (tril, ...): ditto
105 :     * man/band.Rd: ditto
106 : maechler 1349
107 :     2006-08-04 Martin Maechler <maechler@stat.math.ethz.ch>
108 :    
109 :     * R/Matrix.R (head, tail): directly use utils:::head.matrix
110 :     to be up-to-date automatically.
111 :    
112 : maechler 1346 2006-08-03 Martin Maechler <maechler@stat.math.ethz.ch>
113 :    
114 :     * DESCRIPTION (Version): 0.995-13 to be released to CRAN
115 :    
116 :     * DESCRIPTION (Lazydata): no, instead of 'yes' because it fails for:
117 :     * data/CAex.R, inst/external/CAex_slots.rda: replacing data/CAex.rda
118 :     * data/KNex.R, inst/external/KNex_slots.rda: replacing data/KNex.rda
119 :     such that the S4 objects are always created by the current version
120 :     of R and 'Matrix' class definitions.
121 :    
122 : bates 1342 2006-08-01 Douglas Bates <bates@R-project.org>
123 :    
124 :     * R/lmer.R (LMEoptimize method), tests/lmer.R,
125 : maechler 1346 inst/external/test3comp.rda: Added warnings for convergence on
126 : bates 1342 boundary and test cases.
127 :    
128 :     * src/lmer.c (mer_postVar): Modified to return the variances that
129 :     are marginal to the fixed effects, not conditional on them (which
130 :     is what the bVar slot contents represent).
131 :    
132 : bates 1338 2006-07-31 Douglas Bates <bates@R-project.org>
133 :    
134 :     * NAMESPACE, src/lmer.c, R/lmer.R (hatTrace): Add the hatTrace
135 :     function which calls the C function mer_hat_trace2.
136 : maechler 1346
137 : bates 1342 * man/ranef.Rd: Include description of "postVar" argument and
138 :     producing a caterpillar plot.
139 : bates 1338
140 : maechler 1335 2006-07-31 Martin Maechler <maechler@stat.math.ethz.ch>
141 :    
142 :     * NAMESPACE: change "correlation" to "corMatrix"
143 :     * R/AllClass.R: to avoid clash with S3 class in 'nlme'.
144 : bates 1352 * R/dpoMatrix.R: ditto
145 :     * R/lmer.R: ditto
146 : maechler 1335
147 : bates 1338 2006-07-28 Douglas Bates <bates@R-project.org>
148 :    
149 :     * src/lmer.c (internal_mer_RZXinv): Split the calculation of the
150 :     RZXinv slot's contents into a separate internal function that can
151 :     be used in mer_hat_trace.
152 :    
153 : maechler 1331 2006-07-22 Martin Maechler <maechler@stat.math.ethz.ch>
154 :    
155 :     * R/Matrix.R: Coercions "Matrix" -> (sparse|dense)Matrix
156 :     via new smart
157 :     * R/Auxiliaries.R (as_Csparse, as_dense, .M.shapse): new
158 :     utility functions.
159 :    
160 :    
161 : maechler 1330 2006-07-21 Martin Maechler <maechler@stat.math.ethz.ch>
162 :    
163 : maechler 1331 * R/Csparse.R (tril, triu, band): do return *triangular* classed
164 :     matrices when appropriate; band() even symmetric ones.
165 :     (replCmat): extend to potentially all "CsparseMatrix"
166 :     * R/Tsparse.R (replTmat): extend to all "TsparseMatrix"; hence
167 :     allow subassignment for special sparse matrices.
168 :    
169 :     * R/Auxiliaries.R (as_geClass): factor out the .M.kind() functionality
170 :    
171 : maechler 1330 * src/lmer.c (mer_MCMCsamp, glmer_MCMCsamp): new 'verbose'
172 :     argument; in glmer_*(): print only if(verbose).
173 :    
174 :     speed-optimize a few places by moving REAL(.) out of loops.
175 :    
176 :     * src/lmer.h, src/init.h, R/lmer.R: related to above.
177 :    
178 : maechler 1329 2006-07-20 Martin Maechler <maechler@stat.math.ethz.ch>
179 :    
180 :     * R/Matrix.R("["): disable ("Matrix", i = "logical", j = "missing"),
181 :     since that wrongly triggers also for M[ logi , ]
182 :    
183 :     * R/denseMatrix.R: "[" methods now also work e.g. when indexing
184 :     a symmetric matrix that results in a non-symmetric one.
185 :     * R/Auxiliaries.R (as_geClass): new function used in "[" above.
186 :    
187 :     * R/dMatrix.R: make round(M) work as round(M, 0)
188 :    
189 :     * R/dgTMatrix.R (image): coordinate system and axis now use
190 :     1-based indices, not 0-based ones.
191 :    
192 :     * R/Tsparse.R (.ind.prep for "["): get rid of max(<empty>) warning.
193 :     * tests/indexing.R: test it.
194 :    
195 :     * NAMESPACE: export isSymmetric(); has been a generic in "base" for a while;
196 :     * man/isSymmetric-methods.Rd: and document it.
197 :    
198 :     * R/SparseM-conv.R: added coercion methods for some 'SparseM' matrices.
199 :     * man/SparseM-conv.Rd: docu them
200 :    
201 :     * tests/other-pkgs.R: renamed from tests/graph.R and add example
202 :     for 'SparseM' conversions
203 :    
204 :     2006-07-17 Douglas Bates <Douglas.Bates@R-project.org>
205 :    
206 :     * R/Matrix.R (head): added head() and tail() methods.
207 :    
208 :     2006-07-17 Martin Maechler <maechler@stat.math.ethz.ch>
209 :    
210 :     * DESCRIPTION (Version): 0.995-12 released to CRAN
211 :    
212 : maechler 1319 2006-07-15 Martin Maechler <maechler@stat.math.ethz.ch>
213 :    
214 :     * tests/simple.R: add check for correct dsT -> dgT coercion;
215 :     add check for correct printing of symmetric sparse matrices.
216 :    
217 :     * R/Auxiliaries.R (non0ind): return *all* non-0 entry indices also
218 :     for sparse symmetric matrices.
219 :    
220 :     * src/dsTMatrix.c (dsTMatrix_as_dgTMatrix): do not copy the
221 :     diagonal twice.
222 :    
223 : bates 1316 2006-07-11 Douglas Bates <Douglas.Bates@R-project.org>
224 :    
225 :     * src/dsTMatrix.c (dsTMatrix_as_dgTMatrix): Fix a case of INTEGER
226 : maechler 1319 being applied to the x slot (detected by Brian Ripley).
227 : bates 1316
228 : maechler 1315 2006-07-10 Martin Maechler <maechler@stat.math.ethz.ch>
229 :    
230 :     * src/dgCMatrix.c (dgCMatrix_validate): 'p' slot must have correct length.
231 :    
232 :     * R/Auxiliaries.R (isTriC): fix buglet (we were 1-based!)
233 :    
234 :     2006-07-08 Martin Maechler <maechler@stat.math.ethz.ch>
235 :    
236 :     * src/lgCMatrix.c (lgCMatrix_diag): new function
237 :     * R/lgCMatrix.R (diag): for new method
238 :    
239 :     * R/AllClass.R (TsparseMatrix): do use Tsparse_validate
240 :     ==> construction of illegal "*gTMatrix" via new() should
241 :     now be much less easy:
242 :     * tests/Class+Meth.R: assertError() for some illegal "dgT*"
243 :    
244 :     * R/Matrix.R (Matrix): Matrix(0, nrow,ncol) now "goes sparse"
245 :     directly.
246 :     * man/Matrix.Rd: documents it.
247 :    
248 : bates 1311 2006-07-06 Douglas Bates <bates@R-project.org>
249 :    
250 :     * src/pedigree.c (pedigree_inbreeding): Correction in
251 :     initialization. This function is not currently being used and is
252 :     not fully tested.
253 :    
254 : bates 1312 * NAMESPACE, R/{AllClass.R,lmer.R}, src/{init.c,lmer.c}:
255 :     Introduced the glmer class. Added code for mcmcmsamp on glmer
256 :     objects. Modified validity check on pedigree objects to account
257 :     for nonparallel patterns of missingness of parents.
258 : bates 1311
259 : bates 1313 * man/{lmer-class.Rd,mcmcsamp.Rd}: Update documentation for glmer
260 :     class.
261 : maechler 1315
262 :     2006-07-01 Martin Maechler <maechler@stat.math.ethz.ch>
263 :    
264 :     * R/pMatrix.R: coercion pMatrix -> Tsparse
265 :    
266 : bates 1300 2006-06-12 Douglas Bates <bates@R-project.org>
267 :    
268 : maechler 1319 * DESCRIPTION (Version): 0.995-11 released to CRAN
269 :    
270 : bates 1300 * R/lmer.R (mcmcsamp method): Corrected arrangments of names on
271 :     the output from mcmcsamp.
272 :    
273 : bates 1298 2006-06-10 Douglas Bates <bates@R-project.org>
274 :    
275 : bates 1300 * R/lmer.R (simulestimate): added C code for calculating the trace
276 :     of the hat matrix.
277 : bates 1298
278 : maechler 1295 2006-06-09 Martin Maechler <maechler@stat.math.ethz.ch>
279 :    
280 :     * R/diagMatrix.R (setAs): define coercion methods to sparse matrix
281 :     classes.
282 : maechler 1315 * R/sparseMatrix.R etc: multiplication of diagonal and sparse
283 : maechler 1295
284 : maechler 1290 2006-06-08 Martin Maechler <maechler@stat.math.ethz.ch>
285 :    
286 :     * R/dgTMatrix.R (colSums): etc. All four of
287 :     colSums(), rowSums(), colMeans(), rowMeans() now should work for
288 :     all "Matrices".
289 :    
290 : bates 1288 2006-06-01 Douglas Bates <bates@stat.wisc.edu>
291 :    
292 :     * R/lmer.R (panel.ci): Add a reference line at zero and a
293 :     background grid to the qqmath plot of ranef.lmer.
294 :    
295 : bates 1287 2006-05-30 Douglas Bates <bates@stat.wisc.edu>
296 : bates 1284
297 : bates 1287 * R/lmer.R (expandSlash): Functions (non-exported) to allow nested
298 :     grouping factors to be specified in the formula as (1|foo/bar).
299 :    
300 :     2006-05-27 Douglas Bates <bates@stat.wisc.edu>
301 :    
302 : bates 1284 * R/lmer.R (findbars and others): Change check of is.numeric to
303 :     !is.language to resolve the bug reported by Jacob Wegelin.
304 :    
305 :     * src/pedigree.c (pedigree_inbreeding): Initial implementation of
306 :     code to evaluate inbreeding coefficients without calculating T,
307 :     based on code in Sargolzaei and Iwaisaki's paper.
308 :    
309 : bates 1283 2006-05-27 Douglas Bates <bates@stat.wisc.edu>
310 :    
311 :     * R/{lmer.R,AllGeneric.R}, src/{init.c,lmer.[ch]}: Added local
312 :     generic and mer methods for isNested and denomDF. This denomDF was
313 :     an attempt to emulate that in lme but I don't think that makes
314 :     sense. Use the trace of the hat matrix instead.
315 :    
316 : maechler 1271 2006-05-17 Martin Maechler <maechler@stat.math.ethz.ch>
317 :    
318 :     * R/sparseMatrix.R: Matrix <-> graph methods: can no longer use
319 :     the C code depending on a slot structure that's no longer valid.
320 : bates 1352 * src/dgTMatrix.c: ditto (also: src/init.c src/dgTMatrix.h)
321 : maechler 1271
322 :    
323 : bates 1268 2006-05-17 Douglas Bates <bates@stat.wisc.edu>
324 :    
325 :     * R/{AllGeneric.R,Csparse.R},man/band.Rd,NAMESPACE: changed name
326 :     of lowerTriMatrix generic and methods to tril (also upper to triu)
327 :     and added a general band extractor.
328 :    
329 : bates 1267 2006-05-16 Douglas Bates <bates@stat.wisc.edu>
330 :    
331 :     * R/pedigree.R (pedigree): Replace sire and dam values outside the
332 :     allowable range with NAs. Added a corresponding check in the
333 :     validity check for the pedigree class.
334 :    
335 :     * R/[CT]sparse.R ([t]crossprod): The result of single-argument
336 :     crossprod methods now inherits from symmetricMatrix.
337 :    
338 : bates 1265 2006-05-15 Douglas Bates <bates@stat.wisc.edu>
339 :    
340 :     * R/AllGeneric.R (lowerTriMatrix): Added (but did not export)
341 :     generics lowerTriMatrix and upperTriMatrix along with methods for
342 :     the Csparse virtual class. Also added a C function Csparse_band
343 :     that implements these methods by calling cholmod_band.
344 :    
345 : maechler 1264 2006-05-15 Martin Maechler <maechler@stat.math.ethz.ch>
346 :    
347 :     * R/Tsparse.R ("["): column or row subsetting; @Dimnames[k] got
348 :     erased when it was NULL. This led to invalid subselections!
349 :    
350 : bates 1259 2006-04-25 Douglas Bates <bates@stat.wisc.edu>
351 :    
352 :     * R/dtCMatrix.R: avoid coercion of dtCMatrix object to dgCMatrix
353 :     in method for "t" so as not to lose the unit diagonal property.
354 :    
355 : bates 1257 2006-04-19 Douglas Bates <bates@stat.wisc.edu>
356 :    
357 :     * R/lmer.R, R/AllGeneric.R, NAMESPACE: Remove the postVar generic
358 :     and methods. This is now an option to the ranef method for the
359 :     mer class.
360 :    
361 :     * src/cs_utils.c: Ensure that the nz component is -1 for a
362 :     compressed column-oriented matrix. Minor formatting cleanup.
363 :    
364 :     * man/lmer-class.Rd: Document the qqmath method for ranef.lmer
365 :     objects.
366 :    
367 : maechler 1253 2006-04-19 Martin Maechler <maechler@stat.math.ethz.ch>
368 :    
369 :     * R/Auxiliaries.R (diagU2N): new for the solve() methods in
370 :     * R/dtCMatrix.R: where dgC -> dgT coercion now preserves diag = "U".
371 :    
372 : bates 1251 2006-04-15 Douglas Bates <bates@stat.wisc.edu>
373 :    
374 :     * src/cs.[ch],src/cs_utils.[ch] : Added Tim Davis' CSparse library
375 :     in cs.[ch] and utilities to interface to that code in cs_utils.[ch].
376 :    
377 :     * R/dtCMatrix.R, src/dtCMatrix.[ch] : CSparse-based solve methods
378 :     for the dtCMatrix class.
379 : maechler 1253
380 : bates 1247 2006-04-12 Douglas Bates <bates@stat.wisc.edu>
381 :    
382 :     * R/pedigree.R, R/AllClass.R, NAMESPACE: added a pedigree class
383 :     and methods for it.
384 :    
385 : maechler 1245 2006-04-12 Martin Maechler <maechler@stat.math.ethz.ch>
386 :    
387 :     * R/dgCMatrix.R: add storage.mode(.) <- "double" for "matrix"
388 :     arguments, such that M %*% 1:6 now works
389 :     * Tests/matprod.R: test the above
390 :    
391 : bates 1244 2006-04-03 Douglas Bates <bates@stat.wisc.edu>
392 : bates 1243
393 :     * R/lmer.R (qqmath,ranef.lmer-method): added a qqmath method for
394 :     the ranef.lmer class.
395 :    
396 :     * R/AllClass.R, NAMESPACE, R/lmer.R: Added a postVar generic and
397 :     methods to extract the posterior variances from the bVar slot.
398 :    
399 : maechler 1238 2006-03-30 Martin Maechler <maechler@stat.math.ethz.ch>
400 :    
401 :     * R/dtCMatrix.R: allow coercion from dgC* to triangular (dtC*)
402 :     * R/dsCMatrix.R: and symmetric (dsC*) 'Csparse' matrices.
403 :    
404 :     * R/Tsparse.R: Tsparse* -> Csparse* coercion now works and is tested in
405 :     * tests/simple: (extended)
406 :    
407 :     * R/sparseMatrix.R (isTriangular): now using much improved
408 :     * R/Auxiliaries.R (isTriC): new triangularity check for *CMatrix
409 :    
410 : bates 1236 2006-03-23 Douglas Bates <bates@stat.wisc.edu>
411 :    
412 :     * src/dsyMatrix.c (dsyMatrix_as_dspMatrix): Propagate DimNames
413 :     (problem report from Franklin Parlamis). This should be done
414 : maechler 1238 generally.
415 : bates 1236
416 : bates 1234 2006-03-21 Douglas Bates <bates@stat.wisc.edu>
417 :    
418 :     * R/AllClass.R,lmer.R: Change the name of the lmer.ranef class to
419 :     ranef.lmer (like summary.lmer). Add the coef.lmer class and
420 :     update the plot methods.
421 :    
422 : bates 1232 2006-03-20 Douglas Bates <bates@stat.wisc.edu>
423 :    
424 :     * R/lmer.R (resid and ranef methods): Added methods for the
425 :     "residuals" and "resid" generic but only for linear mixed model
426 :     fits. Changed the ranef method to return a list of data frames so
427 :     that the plot methods now work.
428 :    
429 : bates 1230 2006-03-16 Douglas Bates <bates@bates2>
430 :    
431 :     * src/dpoMatrix.c (dpoMatrix_chol): Require n > 0 in call to
432 :     dpotrf - otherwise the BLAS on Mac OS X complains and quits.
433 :    
434 :     * DESCRIPTION (Date): New release
435 :    
436 : maechler 1228 2006-03-15 Martin Maechler <maechler@stat.math.ethz.ch>
437 :    
438 :     * DESCRIPTION (Version): 0.995-6 -- to be released to CRAN
439 :    
440 :     * data/KNex.rda: replacing 'mm' and 'y' by KNex <- list(mm=mm, y=y)
441 :     * man/KNex.Rd: and other help files
442 :     * tests/*.R: several ones needed adaption
443 : bates 1352 * inst/doc/Comparisons.Rnw: ditto
444 : maechler 1228
445 : maechler 1226 2006-03-11 Martin Maechler <maechler@stat.math.ethz.ch>
446 :    
447 :     * R/dgCMatrix.R (replCmat): "[<-" methods for dgCMatrix
448 :    
449 :     * tests/indexing.R: tests for new [<- methods for sparse matrices.
450 :    
451 :     2006-03-10 Martin Maechler <maechler@stat.math.ethz.ch>
452 :    
453 :     * R/dgTMatrix.R (replTmat): "[<-" methods for dgTMatrix
454 :    
455 :     * R/Tsparse.R (.ind.prep): fix out-of-range indexing
456 :    
457 :     2006-03-08 Martin Maechler <maechler@stat.math.ethz.ch>
458 :    
459 :     * R/dMatrix.R: enable things like M [ M < 10 ]
460 :     * R/dgeMatrix.R: implement it
461 :    
462 : maechler 1222 2006-03-06 Martin Maechler <maechler@stat.math.ethz.ch>
463 :    
464 :     * R/AllClass.R: define "summary.mer" and "*.lmer"
465 :     * R/lmer.R (summary): summary(<mer>) computes & returns the above;
466 :     * R/lmer.R (show): now works with summary()
467 :    
468 :     2006-03-04 Martin Maechler <maechler@stat.math.ethz.ch>
469 :    
470 :     * R/dgCMatrix.R: finally direct "Arith" dgC o dgC
471 :     * R/Auxiliaries.R (WhichintersectInd): and other utilities to
472 :     support the above
473 :    
474 : bates 1213 2006-02-07 Douglas Bates <bates@stat.wisc.edu>
475 :    
476 :     * R/lmer.R (lmer): fix initial values of offset and weights for glm.fit.
477 :     Use glmFit$prior.weights for weights in a glmm.
478 :     Allow an option usePQL = FALSE to skip the PQL steps for the
479 :     Laplace method (and, in time, the AGQ method).
480 :    
481 :     * src/lmer.c (mer_factor): Move downdating and factoring of XtX
482 :     into a separate function internal_mer_Xfactor to be able to call
483 :     it from internal_bhat.
484 :    
485 : maechler 1200 2006-01-23 Martin Maechler <maechler@stat.math.ethz.ch>
486 :    
487 :     * tests/Class+Meth.R (tstMatrixClass): function for much better
488 :     testing; now again of all actual classes.
489 :    
490 :     * src/Mutils.c (MAKE_TRIANGULAR_BODY, MAKE_SYMMETRIC_BODY):
491 :     use macros and define make_d_matrix_* and make_i_matrix_*
492 :     where _i_ is for the ldense routines:
493 :    
494 :     * src/ldense.c (ltrMatrix_as_lgeMatrix): provide functions
495 :     * src/ldense.c (lsyMatrix_as_lgeMatrix):
496 :    
497 :     * R/ldenseMatrix.R: use the above in setAs(*,"lgeMatrix")
498 :    
499 :    
500 : maechler 1174 2006-01-16 Martin Maechler <maechler@stat.math.ethz.ch>
501 :    
502 :     * R/Matrix.R (Matrix): has become much "smarter" now auto-producing
503 :     many different kinds of matrices.
504 :     * R/*.R: quite a few new methods were needed for R CMD check with
505 :     new Matrix(). Very good for users playing around.
506 :    
507 :    
508 : maechler 1165 2006-01-15 Martin Maechler <maechler@stat.math.ethz.ch>
509 :    
510 :     * src/dgeMatrix.c (dMatrix_validate): new
511 :     * src/Mutils.c (dense_nonpacked_validate): new
512 :    
513 :     * src/dtrMatrix.c (dtrMatrix_validate): improved/fixed
514 :    
515 :    
516 :     2006-01-14 Douglas Bates <bates@stat.wisc.edu>
517 :    
518 :     * R/AllClass.R (compMatrix), (generalMatrix): new virtual classes
519 :    
520 : bates 1123 2006-01-07 Douglas Bates <bates@stat.wisc.edu>
521 : bates 1119
522 : maechler 1127 * DESCRIPTION (Version): 0.99-6 released to CRAN
523 :    
524 : bates 1119 * src/dgBCMatrix.c (cscb_trcbsm): Fix due to Peter Dalgaard for
525 :     segfault in cases with multiple non-nested grouping factors.
526 :    
527 : maechler 1109 2006-01-03 Martin Maechler <maechler@stat.math.ethz.ch>
528 :    
529 :     * DESCRIPTION (Version): 0.99-4 to be released to CRAN
530 :     (Depends): also on 'utils'
531 :    
532 :     * R/AllClass.R (diagonalMatrix): new class with "ddi*" and "ldi*"
533 :     * R/diagMatrix.R (Diagonal): constructor and methods for
534 :     diagonal matrices
535 :    
536 :     * R/ltTMatrix.R: new "minimal methods"
537 :    
538 : maechler 1091 2005-12-12 Martin Maechler <maechler@stat.math.ethz.ch>
539 :    
540 :     * R/AllGeneric.R (tcrossprod): 2-argument version; here, and for
541 :     all methods (and help files).
542 :    
543 : maechler 1084 2005-12-09 Martin Maechler <maechler@stat.math.ethz.ch>
544 :    
545 :     * R/Auxiliaries.R (dimNamesCheck): fixed thinko -> bug
546 :     for case (dimn. op no_dimn.)
547 :    
548 :     2005-11-14 Douglas Bates <bates@stat.wisc.edu>
549 :    
550 : maechler 1174 * DESCRIPTION (Version): 0.99-2 released to CRAN
551 : maechler 1084
552 : bates 988 2005-10-21 Douglas Bates <bates@stat.wisc.edu>
553 :    
554 :     * R/lmer.R (simulate method): Fixed a drop=FALSE problem reported
555 :     by Julian Faraway.
556 :    
557 : maechler 976 2005-10-06 Martin Maechler <maechler@stat.math.ethz.ch>
558 :    
559 :     * R/Auxiliaries.R (try_as): new utility
560 :     * R/sparseMatrix.R: use try_as() in coercion to original class
561 :    
562 : maechler 956 2005-09-30 Martin Maechler <maechler@stat.math.ethz.ch>
563 :    
564 :     * src/dgCMatrix.c (double_to_csc): and dgeMatrix_to_csc()
565 :    
566 :     2005-09-29 Martin Maechler <maechler@stat.math.ethz.ch>
567 :    
568 :     * R/Auxiliaries.R (dimNamesCheck): added
569 :    
570 :     * R/Matrix.R (as.array), (as.vector): new
571 :    
572 : maechler 954 2005-09-28 Martin Maechler <maechler@stat.math.ethz.ch>
573 :    
574 :     * R/Matrix.R (Matrix): get logical argument 'sparse' with a smart
575 : maechler 956 default.
576 :     * R/AllClass.R: move 'factors' slot toplevel "Matrix";
577 :     "pMatrix" now contains "sparseMatrix"
578 : maechler 954
579 : maechler 948 2005-09-26 Martin Maechler <maechler@stat.math.ethz.ch>
580 :    
581 :     * tests/Class+Meth.R: new tests; t(t(m)) == m
582 :    
583 :     * src/dtCMatrix.c (tsc_transpose): add forgotten "diag" slot
584 :    
585 :     * src/dsTMatrix.c (dsTMatrix_as_dsCMatrix): bad typo (segfault!)
586 :     * src/dtTMatrix.c (dtTMatrix_as_dtCMatrix): new
587 :    
588 :     * R/dspMatrix.R: typo in "t" method
589 :    
590 : maechler 925 2005-09-18 Douglas Bates <bates@wisc.edu>
591 :    
592 :     * R/AllClass.R (TsparseMatrix), CsparseM* and RsparseM*
593 :     * R/Tsparse.R: instead of R/gTMatrix.R
594 :     * R/Csparse.R: new
595 :     * src/Tsparse.c (Tsparse_to_Csparse): new; -> cholmod_()
596 :     * src/Tsparse.c: new; many trivial methods calling cholmod_()
597 :     * src/Csparse.c (Csparse_to_Tsparse), transpose, (mat|cross)prod:
598 :     via cholmod
599 :    
600 :     2005-09-16 Martin Maechler <maechler@stat.math.ethz.ch>
601 :    
602 :     * R/Auxiliaries.R (non0ind): new function using new C code
603 :     * src/dgCMatrix.c (compressed_non_0_ij): new utility
604 :    
605 : bates 917 2005-09-15 Douglas Bates <bates@localhost.localdomain>
606 :    
607 :     * src/chm_common.h: header file required by all C sources that
608 : maechler 1174 call CHOLMOD functions. It defines a cholmod_common structure
609 : bates 917 called 'c' whose address is passed as the last argument to
610 :     (virtually) every CHOLMOD function.
611 :    
612 :     * src/Pattern.c: Simple example of the use of CHOLMOD.
613 :    
614 :     * src/init.c: initialize and finalize the cholmod_common structure.
615 :    
616 :     * src/Makefile: Added source packages CHOLMOD UMFPACK AMD COLAMD
617 :     LDL and CCOLAMD from the U. of Florida sparse matrix library.
618 :    
619 : maechler 908 2005-09-08 Martin Maechler <maechler@stat.math.ethz.ch>
620 :    
621 :     * inst/test-tools.R: new file collecting the utility functions used
622 :     in ./tests/*.R
623 :    
624 :     * R/ddenseMatrix.R (cbind2): new methods for "numeric" and "matrix"
625 :     * R/Matrix.R (cbind2): methods for NULL and missing
626 :    
627 : maechler 886 2005-08-31 Martin Maechler <maechler@stat.math.ethz.ch>
628 :    
629 :     * R/AllClass.R: new "index" class for "[" and "[<-":
630 :     First cut at "symmetricMatrix" and "triangularMatrix"
631 :     * R/gTMatrix.R (.ind.prep): new function;
632 : maechler 1174 Logical and character indexing now work too.
633 : maechler 886 * R/Matrix.R: cheap "[<-" methods for denseMatrix now work
634 :     * tests/indexing.R: new, including *.Rout.save
635 :     * tests/dgTMatrix.R: new
636 :    
637 : bates 876 2005-08-29 Douglas Bates <bates@wisc.edu>
638 :    
639 :     * src/dgTMatrix.c (graphNEL_as_dgTMatrix): Corrected the position
640 :     indicator pos not being updated. Also enforced upper triangular
641 :     for symmetric case. Need to coerce edges component of elements of
642 :     edge list - grr! (Why don't they define their classes cleanly?)
643 :    
644 : maechler 871 2005-08-26 Martin Maechler <maechler@stat.math.ethz.ch>
645 :    
646 :     * R/Matrix.R: added first "[<-" methods; not yet functional
647 : bates 1352 * R/denseMatrix.R: ditto
648 : maechler 871 * man/Subassign-methods.Rd: new help file for these
649 :    
650 :     2005-08-25 Martin Maechler <maechler@stat.math.ethz.ch>
651 :    
652 :     * DESCRIPTION (Version): 0.98-6
653 :    
654 :     * R/denseMatrix.R: new file for "[" fallback methods for all dense
655 :     matrices.
656 :    
657 : maechler 868 2005-08-19 Martin Maechler <maechler@stat.math.ethz.ch>
658 :    
659 :     * src/lgCMatrix.c (lcsc_to_matrix): new; need for
660 :     as( <logical>, "matrix")
661 :    
662 :     * R/pMatrix.R: coercion to "lgTMatrix"
663 :    
664 :     * R/gTMatrix.R: new virtual class to define "[" methods for.
665 :     * man/gTMatrix-class.Rd:
666 :     * General slight re-organization of where "[" methods are defined.
667 :     more to come.
668 :    
669 : maechler 871 2005-08-18 Douglas Bates <bates@wisc.edu>
670 : maechler 868
671 : maechler 1174 * DESCRIPTION (Version): 0.98-5 released to CRAN
672 : maechler 871
673 :     * src/dgTMatrix.c (graphNEL_as_dgTMatrix): add first graphNEL methods
674 :     * .....
675 :    
676 : bates 863 2005-08-18 Douglas Bates <bates@localhost.localdomain>
677 :    
678 :     * R/lmer.R: Corrected naming scheme in mcmcsamp to work with lmer
679 :     or glmer objects.
680 :    
681 : maechler 860 2005-08-17 Martin Maechler <maechler@stat.math.ethz.ch>
682 :    
683 :     * DESCRIPTION (Version): 0.98-4 : upload to CRAN
684 :    
685 :     2005-08-16 Douglas Bates <bates@localhost.localdomain>
686 :    
687 :     * R/HBMM.R: finish re-writing R-only code.
688 :    
689 : bates 854 2005-08-15 Douglas Bates <bates@localhost.localdomain>
690 :    
691 :     * man/externalFormats.Rd: move documentation for writeHB and
692 :     writeMM here.
693 :    
694 :     * src/mmio.c: replace inclusion of <malloc.h> by <stdlib.h>
695 :     (suggested by Paul Roecker).
696 :    
697 :     * tests/validObj.R (assertError): Comment out test that is failing
698 :     after recent changes in r-devel.
699 :    
700 : maechler 860
701 : maechler 848 2005-08-11 Martin Maechler <maechler@stat.math.ethz.ch>
702 :    
703 :     * R/AllClass.R: intermediate virtual class "denseMatrix"
704 :     * man/denseMatrix-class.Rd
705 :     * NAMESPACE: export it, and also export
706 :     * man/unused-classes.Rd: "iMatrix", "zMatrix" and "ldenseMatrix"
707 :    
708 : bates 846 2005-08-10 Douglas Bates <bates@wisc.edu>
709 :    
710 : maechler 848 * DESCRIPTION (Version): 0.98-3 to CRAN
711 :    
712 : bates 846 * src/dtrMatrix.c (dtrMatrix_validate): fixed up validation and
713 :     matrix_solve code (which was really, really wrong).
714 :    
715 : bates 835 2005-08-07 Douglas Bates <bates@wisc.edu>
716 : maechler 834
717 :     * DESCRIPTION (Version): 0.98-2
718 :    
719 :     * R/HBMM.R (readHB), (readMM): read Matrix Market formats
720 :    
721 :     * R/lmer.R (abbrvNms): new
722 :     * R/lmer.R (mcmcsamp): allow transformed parameters
723 : bates 835 * src/HBMM.c (Matrix_writeMatrixMarket): Added read/write routines
724 :     for the Harwell-Boeing and the MatrixMarket formats.
725 : maechler 834
726 :     2005-08-04 Martin Maechler <maechler@stat.math.ethz.ch>
727 :    
728 :     * man/dtrMatrix-class.Rd: add examples
729 : bates 835 * man/dtpMatrix-class.Rd: ditto; plus note about PROBLEM
730 : maechler 834
731 :     * TODO: note the dtpMatrix (docu) bug
732 :    
733 :     * R/zzz.R (.onLoad): assignInNamespace("as.matrix", *, "base")
734 :     in order to ensure that new as.matrix() is used by old functions,
735 :     e.g., svd(), qr(), eigen(), dist(),..;
736 :     apply(), also matplot() or pairs().
737 :    
738 :    
739 :     2005-08-03 Martin Maechler <maechler@stat.math.ethz.ch>
740 :    
741 :     * R/lmer.R: add 'fixme' comments and move the linear vs glm check;
742 :     add comments about 'control' / lmerControl() arguments
743 :    
744 : bates 835 2005-07-27 Douglas Bates <bates@wisc.edu>
745 : bates 820
746 : bates 835 * man/sleepstudy.Rd: Added the sleep data set.
747 : maechler 1174 * DESCRIPTION (Version): 0.98-1 released to CRAN
748 : bates 820
749 : bates 835 2005-07-12 Douglas Bates <bates@wisc.edu>
750 : maechler 834 * man/sleepstudy.Rd: Added the sleep data set.
751 :    
752 : bates 809 * R/lmer.R (glmmMCMC): Added PACKAGE = "Matrix" in a couple of
753 :     .Call calls that were producing spurious output.
754 :    
755 : bates 835 2005-07-05 Douglas Bates <bates@wisc.edu>
756 : bates 801
757 :     * R/lmer.R (lmer): stored updated variance component estimates in
758 :     mer object for the generalized model. (Bug reported by Renaud
759 :     Lancelot).
760 :    
761 : bates 835 2005-07-03 Douglas Bates <bates@wisc.edu>
762 : bates 794
763 :     * src/lmer.c (glmer_devAGQ): Added AGQ for single grouping factor,
764 :     unidimensional case.
765 :    
766 : bates 835 2005-06-08 Douglas Bates <bates@wisc.edu>
767 : maechler 791
768 :     * DESCRIPTION (Version): 0.96-1
769 :    
770 : maechler 1174 * moved lmer-class' R and C code moved from lme4 to here
771 : maechler 791
772 : bates 835 2005-06-04 Douglas Bates <bates@wisc.edu>
773 : bates 763
774 :     * R/dgCMatrix.R: Call to csc_matrix_mm used undefined arguments
775 :     (reported by Guissepe Ragusa <gragusa@ucsd.edu>)
776 :    
777 : bates 835 2005-06-02 Douglas Bates <bates@wisc.edu>
778 : bates 763
779 :     * src/Makefile.win: Forgot to update this when Makefile changed.
780 :    
781 : bates 835 2005-05-11 Douglas Bates <bates@wisc.edu>
782 : bates 726
783 :     * src/dgCMatrix.c (csc_transpose): Simplified function fixing a
784 :     bug reported by Kurt Hornik and Michael Hahsler.
785 :    
786 : bates 835 2005-05-10 Douglas Bates <bates@wisc.edu>
787 : bates 725
788 :     * src/lgCMatrix.c (Matrix_lgClgCmm): Implementation of methods for
789 :     logical sparse matrices. These will also be used in the symbolic
790 :     analysis for lmer objects.
791 :    
792 :     * src/dsCMatrix.c (dsCMatrix_matrix_solve): Copied the dimensions
793 :     of b to the result. Fixes bug reported by Jean.Coursol@math.u-psud.fr
794 : maechler 791
795 : bates 835 2005-05-06 Douglas Bates <bates@wisc.edu>
796 : bates 714
797 :     * src/dgeMatrix.c (dgeMatrix_colsums): Added an implementation of
798 :     colMeans, colSums, rowMeans and rowSums.
799 :    
800 : bates 835 2005-04-18 Douglas Bates <bates@wisc.edu>
801 : bates 692
802 :     * src/lgCMatrix.[ch]: code for _validate method and stub for
803 :     multiplication operation.
804 :    
805 :     * src/dgeMatrix.c (dgeMatrix_matrix_solve): Passing wrong argument
806 :     to dgetrs.
807 :    
808 :     * src/init.c: Fix cut-and-paste error in definition of
809 :     dgeMatrix_matrix_solve
810 :    
811 :     * src/{many files}: Tighten code by using ALLOC_SLOT.
812 :    
813 : bates 835 2005-04-15 Douglas Bates <bates@wisc.edu>
814 : bates 692
815 :     * R/AllClass.R: Add lgTMatrix and lgCMatrix classes
816 :    
817 :     * DESCRIPTION: Eliminate import of stats.
818 :    
819 : maechler 791
820 : bates 835 2005-04-06 Douglas Bates <bates@wisc.edu>
821 : bates 692
822 :     * R/AllClass.R : add logical sparse matrix classes
823 :    
824 : maechler 687 2005-04-01 Martin Maechler <maechler@stat.math.ethz.ch>
825 :    
826 :     * R/dgTMatrix.R: add "[" method for triplet matrices
827 :     * R/sparseMatrix.R: and other sparse ones; --> add show() for sparse
828 :    
829 : bates 835 2005-03-31 Douglas Bates <bates@wisc.edu>
830 : maechler 687
831 :     * DESCRIPTION (Version): release 0.95-5 to CRAN
832 :    
833 :     * R/dMatrix.R: add %*%, crossprod and solve "fallback" methods
834 :     * R/sparseMatrix.R: %*%, crossprod()
835 :     * R/dgeMatrix.R: more "fallback" methods for numeric/dense matrices
836 :     * man/*.Rd: move method definitions to 'Matrix' and 'dMatrix'
837 :     * src/lmer.c (lmer_fitted): fix thinko
838 :    
839 : maechler 676 2005-03-26 Martin Maechler <maechler@stat.math.ethz.ch>
840 :    
841 :     * R/AllClass.R: add two virtual sparse classes ``on top''
842 :    
843 :     2005-03-24 Martin Maechler <maechler@stat.math.ethz.ch>
844 :    
845 :     * R/AllClass.R (setClass): use "VIRTUAL" for the virtual classes;
846 :     correspondingly fix examples and tests/ since new()
847 :     doesn't work for virtual classes.
848 :    
849 : maechler 658 2005-03-17 Martin Maechler <maechler@stat.math.ethz.ch>
850 :    
851 :     * R/Matrix.R (as.matrix): method and one for unname()
852 :     * tests/dpoMatrix.R: tests should now be less platform dependent;
853 :     also run for R 2.1.0; using as.matrix()
854 :    
855 : bates 835 2005-03-15 Douglas Bates <bates@wisc.edu>
856 : maechler 658
857 :     * R/pMatrix.R: "pMatrix" class added
858 :     * ....
859 :    
860 : bates 835 2005-03-14 Douglas Bates <bates@wisc.edu>
861 : bates 645
862 :     * R/dtpMatrix.R: Add unpack method and an example.
863 :    
864 :     * src/dsyMatrix.c (dsyMatrix_trf): Add BunchKaufman factorization
865 :     of general symmetric matrices and associated S4 methods.
866 :    
867 : maechler 658 2005-03-10 Martin Maechler <maechler@stat.math.ethz.ch>
868 :     +
869 :     2005-03-05 Martin Maechler <maechler@stat.math.ethz.ch>
870 :    
871 :     * R/dgeMatrix.R (setAs): and many other files: more coercion,
872 :     crossprod() and "%*%" methods added; tests, too.
873 :     * tests/matprod.R: new, for testing these
874 :    
875 : bates 835 2005-03-03 Douglas Bates <bates@wisc.edu>
876 : bates 599
877 :     * src/lmer.c (lmer_fitted): Added.
878 :    
879 : bates 835 2005-03-02 Douglas Bates <bates@wisc.edu>
880 : bates 596
881 :     * R/dsTMatrix.R: Conversion from dsTMatrix to dsCMatrix
882 :    
883 : bates 835 2005-02-28 Douglas Bates <bates@wisc.edu>
884 : bates 582
885 :     * src/*.c,po/,inst/po: Internationalization and localization of
886 :     the package.
887 :    
888 :     * src/ldl.[ch]: Removed these as their contents are referenced in the
889 :     R_ldl.c file.
890 :    
891 :     * src/flame.[ch]: Removed these source files.
892 : maechler 658
893 : bates 582 * src/dtrMatrix.c (make_array_triangular): Move to Mutils
894 :    
895 :     * src/LU.[ch],src/init.c: absorb in factorizations
896 :    
897 :     * src/Mutils.h: prepare for internationalization
898 :    
899 :     * src/cblas.h: move the enum definitions to Mutils.h and remove
900 :     this file
901 :    
902 : maechler 578 2005-02-26 Martin Maechler <maechler@stat.math.ethz.ch>
903 :    
904 : maechler 579 * R/dgeMatrix.R: provide "dimnames" and "dimnames<-" methods
905 :    
906 :     * R/dtrMatrix.R: fix t() method
907 :    
908 : maechler 578 * R/dgeMatrix.R: define group methods "Arith", "Math", "Math2"
909 : maechler 658 * NAMESPACE: export them (and import generics from "methods")
910 : maechler 578 * tests/group-methods.R : and test them.
911 :    
912 :     * src/dtrMatrix.c (dtrMatrix_as_dgeMatrix): prevent seg.fault in
913 :     border case
914 :    
915 :     2005-02-24 Douglas Bates <bates@stat.wisc.edu>
916 :    
917 : maechler 658 * DESCRIPTION (Version): 0.95-2 released to CRAN
918 : maechler 578
919 :     * src/dgBCMatrix.c:
920 :     * src/lmer.c: many changes
921 :     * ...
922 :    
923 : maechler 512 2005-02-04 Martin Maechler <maechler@stat.math.ethz.ch>
924 :    
925 :     * R/Matrix.R: add more sophisticated show() method.
926 :    
927 : maechler 578 2005-02-02 Douglas Bates <bates@stat.wisc.edu>
928 :    
929 :     * */* : almost complete reorganization of classes.
930 :    
931 : bates 835 2005-01-26 Douglas Bates <bates@wisc.edu>
932 : bates 460
933 :     * R/AllGeneric.R: Added matrix exponential generic expm and a method
934 :     for the geMatrix class.
935 :    
936 : bates 835 2005-01-24 Douglas Bates <bates@wisc.edu>
937 : bates 460
938 :     * src/Makefile (clean): Remove *.a and *.so
939 :    
940 :     * man/cscBlocked-class.Rd: Remove reference to the lmer-class.
941 :    
942 : bates 835 2005-01-23 Douglas Bates <bates@wisc.edu>
943 : bates 460
944 : maechler 658 * src/lmer.c (Lind): Definition of Lind was backwards. This only
945 : bates 460 had an effect in cases with more than 2 grouping factors.
946 :    
947 : bates 835 2005-01-03 Douglas Bates <bates@wisc.edu>
948 : bates 415
949 :     * src/lmeRep.c (lmer_variances): change from lmeRep to lmer
950 :    
951 : bates 835 2004-12-23 Douglas Bates <bates@wisc.edu>
952 : bates 410
953 :     * src/init.c (R_init_Matrix): Reorder calls to R_registerRoutines
954 :     and R_useDynamicSymbols (suggested by B.D.Ripley).
955 :    
956 : bates 835 2004-12-14 Douglas Bates <bates@wisc.edu>
957 : bates 392
958 :     * R/sscMatrix.R: Add determinant methods
959 :    
960 :     * src/triplet.[ch],src/init.c (triplet_to_matrix): Add a coercion
961 :     for tripletMatrix to matrix.
962 :    
963 : bates 835 2004-12-13 Douglas Bates <bates@wisc.edu>
964 : bates 388
965 : bates 392 * R/AllClass.R (.onLoad): Eliminate the bbCrosstab class, which is
966 :     no longer used.
967 :    
968 : bates 388 * src/R_ldl.c: Created an R-specific version of the ldl.[ch] files
969 :     with dynamic allocation of scratch arrays.
970 :    
971 :     * src/ssclme.c (ssclme_copy_ctab): Fixed bug in creation of ZtZ
972 :     for multivariate random effects with multiple grouping factors.
973 :     Fixes part but not all of #15.
974 :    
975 : bates 835 2004-12-03 Douglas Bates <bates@wisc.edu>
976 : bates 375
977 :     * src/lmeRep.c (lmeRep_factor): order of operations for multiple
978 :     scalar grouping factors corrected.
979 :    
980 : bates 835 2004-11-29 Douglas Bates <bates@wisc.edu>
981 : bates 375
982 :     * src/bCrosstab.c: remove diag_update which is no longer used
983 :    
984 : bates 835 2004-11-16 Douglas Bates <bates@wisc.edu>
985 : bates 350
986 :     * src/Metis_utils.c: Move metis.h include to C sources so that the
987 :     .h file can be included.
988 :    
989 : bates 835 2004-11-12 Douglas Bates <bates@wisc.edu>
990 : bates 342
991 : bates 350 * src/LU.c,geMatrix.c,trMatrix.c, etc.:
992 : bates 342 Complete allocation of slots in NEW_OBJECT.
993 :    
994 :     * src/Mutils.h: Moved list of symbols to an include file
995 :    
996 : bates 835 2004-11-11 Douglas Bates <bates@wisc.edu>
997 : bates 342
998 :     * src/geMutils.c (Matrix_init): remove unused function
999 :    
1000 : bates 835 2004-11-10 Douglas Bates <bates@wisc.edu>
1001 : bates 342
1002 :     * src/cscMatrix.c (csc_to_imagemat): removed unused function
1003 :    
1004 : bates 835 2004-11-05 Douglas Bates <bates@wisc.edu>
1005 : bates 327
1006 :     * src/Makefile.win (SOURCES_C): Keep consistent with Makefile
1007 :    
1008 : bates 835 2004-10-27 Douglas Bates <bates@wisc.edu>
1009 : bates 303
1010 :     * R/pdmatrix.R: remove PACKAGE="Matrix" in .Call calls
1011 :    
1012 : bates 835 2004-10-04 Douglas Bates <bates@wisc.edu>
1013 : bates 296
1014 :     * src/init.c: Created R_init_Matrix and added registration of C
1015 :     routines.
1016 :    
1017 : bates 835 2004-10-02 Douglas Bates <bates@wisc.edu>
1018 : bates 283
1019 :     * R/tripletMatrix.R: Force a require(lattice) for the image methods.
1020 :    
1021 : bates 835 2004-06-15 Douglas Bates <bates@wisc.edu>
1022 : bates 229
1023 :     * man/trMatrix-class.Rd: Escape the % chars in .Rd files.
1024 :    
1025 : bates 111 2004-04-20 Douglas Bates <bates@stat.wisc.edu>
1026 :    
1027 :     * src/Makefile.win ($(SHLIB)): Modifications per Uwe Ligges.
1028 :    
1029 : bates 109 2004-04-19 Douglas Bates <bates@stat.wisc.edu>
1030 :    
1031 :     * src/ssclme.c (ssclme_update_mm): fix logic error in
1032 :     ssclme_update_mm
1033 :    
1034 : bates 105 2004-04-18 Douglas Bates <bates@stat.wisc.edu>
1035 :    
1036 :     * src/ssclme.c (ssclme_coef, ssclme_coefGets): Create consistency
1037 :     in the order of unconstrained and constrained parameters.
1038 :     (ssclme_gradient): Added the gradients (not yet correct for
1039 :     multidimensional, unconstrained case).
1040 :    
1041 : bates 78 2004-04-14 Douglas Bates <bates@stat.wisc.edu>
1042 :    
1043 :     * src/ssclme.c (ssclme_EMsteps): Fix logic in REML update
1044 :    
1045 :     * src/Makefile.win: Remove unneeded ranlib call
1046 :    
1047 : bates 71 2004-04-12 Douglas Bates <bates@stat.wisc.edu>
1048 :    
1049 :     * DESCRIPTION (Version): New release
1050 :    
1051 :     * src/Makefile.win: Update Makefile.win to umfpack removal.
1052 :    
1053 : bates 49 2004-04-05 Douglas Bates <bates@bates2_home>
1054 :    
1055 :     * src/triplet_to_col.c: Create triplet_to_col as a native
1056 : maechler 658 function, not the version from umfpack. There were problems with
1057 : bates 49 the configuration of UMFPACK for 64-bit processors and there was
1058 :     only one umfpack routine being used so I moved it here.
1059 :    
1060 : bates 45 2004-04-04 Douglas Bates <bates@bates2_home>
1061 :    
1062 :     * src/ssclme.c (ssclme_variances): New function.
1063 :    
1064 : bates 28 2004-03-28 Douglas Bates <bates@bates2_home>
1065 :    
1066 :     * src/ssclme.c (ssclme_fitted): Added function.
1067 :    
1068 : bates 22 2004-03-27 Douglas Bates <bates@bates2_home>
1069 :    
1070 :     * src/ssclme.c (ssclme_transfer_dimnames): Add new function to
1071 :     store the dimnames in the XtX and bVar slots
1072 :     (ssclme_update_mm): Change the dimensions of the bVar slot
1073 :     components and the returned value from ssclme_ranef.
1074 :    
1075 : bates 10 2004-03-18 Douglas Bates <bates@stat.wisc.edu>
1076 :    
1077 :     * R/{pdMat.R,pdIdent.R,pdLogChol.R,pdMatrixLog.R,pdNatural.R},
1078 :     src/{pdMat.c,pdIdent.c,pdLogChol.c,pdNatural.c},
1079 :     tests/{pdCompSymm.R,pdDiag.R,pdIdent.R,pdLogChol.R,pdNatural.R},
1080 :     man/{pdMat-class.Rd,pdmatrix-class.Rd,corrmatrix-class.Rd,
1081 :     pdDiag-class.Rd,pdIdent-class.Rd,pdNatural-class.Rd,
1082 :     pdLogChol-class.Rd,coefGets.Rd,pdCompSymm-class.Rd,
1083 :     pdfactor-class.Rd,pdFactor.Rd,pdMatrix.Rd,
1084 :     pdBlocked-class.Rd},AllClass.R,AllGeneric.R:
1085 :     Moved the pdMat classes from the lme4 package.
1086 :    
1087 :     2004-03-02 Douglas Bates <bates@stat.wisc.edu>
1088 :    
1089 :     * man/ssclme-class.Rd: Update definition and documentation of the
1090 :     ssclme class to include the DIsqrt slot.
1091 :    
1092 :     * src/ssclme.c (ssclme_deviance): Modify order of computation
1093 :     (much faster using dsyrk, a level 3 BLAS routine).
1094 :    
1095 :     * src/Makefile (SUBLIBS): Change definition (K. Hornik)
1096 :    
1097 :     2004-02-28 Douglas Bates <bates@stat.wisc.edu>
1098 :    
1099 :     * tests/ssclme.R: Modify the test to account for the permutation
1100 :     of the levels of the grouping factors.
1101 :    
1102 :     2004-02-23 Douglas Bates <bates@stat.wisc.edu>
1103 :    
1104 :     * R/ssclme.R,src/ssclme.c (ssclme): Move slots of sscCrosstab slot
1105 :     directly into the ssclme class definition.
1106 :    
1107 :     2004-02-22 Douglas Bates <bates@stat.wisc.edu>
1108 :    
1109 :     * DESCRIPTION (Date): New release
1110 :    
1111 :     * man/ssclme-class.Rd: new file.
1112 :    
1113 :     * src/ssclme.c (ssclme_loglik): major revisions in design. It
1114 :     works and it's fast!
1115 :    
1116 :     2004-02-17 Douglas Bates <bates@stat.wisc.edu>
1117 :    
1118 :     * src/taucs/Makefile.win (lib): Change "ar" to "$(AR)" (B.Ripley)
1119 :    
1120 :     2004-02-16 Douglas Bates <bates@stat.wisc.edu>
1121 :    
1122 :     * DESCRIPTION (Date): New release
1123 :    
1124 :     * NAMESPACE: Don't export ssclme.
1125 :    
1126 :     * data/ScotsSec.rda, man/ScotsSec.Rd: Add Scottish secondary
1127 :     school data.
1128 :    
1129 :     2004-02-11 Douglas Bates <bates@stat.wisc.edu>
1130 :    
1131 :     * src/sscCrosstab.c (sscCrosstab): Added a row to the incidence to
1132 :     keep track of the fixed-effects and the response. Counts also
1133 :     gets an extra element, which is always one.
1134 :    
1135 :     * src/ldl.c: Include these routines from Tim Davis' LDL package.
1136 :    
1137 :     2004-02-10 Douglas Bates <bates@stat.wisc.edu>
1138 :    
1139 :     * src/cscMatrix.c (csc_transpose): new function
1140 :    
1141 :     * src/Mutils.c (csc_sort_columns): perm/iperm confusion corrected
1142 :     (csc_components_transpose): new function
1143 :    
1144 :     2004-02-06 Douglas Bates <bates@stat.wisc.edu>
1145 :    
1146 :     * src/triplet.c (triplet_validate): Fix Dim slot on generated
1147 :     triplets
1148 :    
1149 :     2004-01-30 Douglas Bates <bates@stat.wisc.edu>
1150 :    
1151 :     * R/sscCrosstab.R (sscCrosstab): Added sscCrosstab generator function.
1152 :    
1153 :     * src/LU.h (MATRIX_LU_H): Add #ifndef #define ... #endif to this
1154 :     and all other .h files in src.
1155 :    
1156 :     * src/Makefile.win: This and other Makefile.win files contributed
1157 :     by Brian Ripley.
1158 :    
1159 :     2004-01-27 Douglas Bates <bates@stat.wisc.edu>
1160 :    
1161 :     * R/syMatrix.R: Added methods for "%*%".
1162 :    
1163 :     * R/Hilbert.R (Hilbert): Changed Hilbert function to return a
1164 :     poMatrix object.
1165 :    
1166 :     2004-01-26 Douglas Bates <bates@stat.wisc.edu>
1167 :    
1168 :     * man/sscChol-class.Rd,man/mm.Rd,man/y.Rd: Added man pages.
1169 :    
1170 :     2004-01-25 Douglas Bates <bates@bates2_home>
1171 :    
1172 :     * inst/doc/Introduction.Rnw,Comparisons.Rnw: Added vignettes.
1173 :    
1174 :     * R/csc.R: Convert all cscMatrix classes to use Dim slot instead
1175 :     of nrow.
1176 :    
1177 :     2003-12-31 Douglas Bates <bates@stat.wisc.edu>
1178 :    
1179 :     * src/taucs/taucs.h: Moved taucs.h, amd.h, and umfpack.h into
1180 :     subdirectories.
1181 :    
1182 :     2003-12-08 Douglas Bates <bates@stat.wisc.edu>
1183 :    
1184 :     * src/taucs.h: Accidently referred to global header files
1185 :     instead of local files.
1186 :    
1187 :     2003-12-04 Douglas Bates <bates@stat.wisc.edu>
1188 :    
1189 :     * R/AllClass.R: Lots of changes. Removed all the lapack++ code
1190 :     and methods and replaced all classes with S4 classes.
1191 :    
1192 :     2003-04-19 Douglas Bates <bates@stat.wisc.edu>
1193 :    
1194 :     * R/det.R,man/det.Rd: Change name of det generic to determinant
1195 :    
1196 :     * src/R_LapackPP.cc: Change method of calculating determinants
1197 :    
1198 :     2003-02-03 Douglas Bates <bates@stat.wisc.edu>
1199 :    
1200 :     * DESCRIPTION (Version): removed empty data directory as requested
1201 :     by CRAN maintainers. Changed version number and date.
1202 :    
1203 :     2002-10-23 Douglas Bates <bates@stat.wisc.edu>
1204 :    
1205 :     * src/laindex.h: Applied patches from Brian Ripley for compilation
1206 :     under Windows.
1207 :    
1208 :     * Added configure.win and src/Makevars.win as requested by Brian
1209 :     Ripley.
1210 :    
1211 :     2002-05-03 Douglas Bates <bates@stat.wisc.edu>
1212 :    
1213 :     * src/lamatrix.h: Removing pre-1.2.0 compatibility code per Kurt
1214 :     Hornik.
1215 :    
1216 :     2002-04-24 Douglas Bates <bates@stat.wisc.edu>
1217 :    
1218 :     * configure.ac: Replaced configure.in with configure.ac
1219 :     contributed by Kurt Hornik.
1220 :    
1221 :     * aclocal.m4 (ac_clean_files): Replaced this with Kurt Hornik's
1222 :     version for R-1.5.0
1223 :    
1224 : maechler 512
1225 : bates 10 2001-12-10 Douglas Bates <bates@stat.wisc.edu>
1226 :    
1227 :     * man/eigen.Rd: Removed the .Alias in the example

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