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Annotation of /pkg/ChangeLog

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1 : bates 1414 2006-08-22 Douglas Bates <bates@R-project.org>
2 :    
3 :     * src/Mutils.c (dup_mMatrix_as_dgeMatrix): updated for general
4 :     types of classed Matrices, matrices or numeric or logical vectors.
5 :     * src/init.c: register dup_mMatrix_as_dgeMatrix for coercions.
6 :    
7 : bates 1405 2006-08-21 Douglas Bates <bates@R-project.org>
8 :    
9 :     * src/lmer.c (internal_mer_RZXinv): Fix memory leak caught by
10 :     valgrind.
11 : bates 1411 * tests/matprod.R: Add tests to verify that 'solve' and '%*%' are
12 :     inverses.
13 :     * src/sparseQR.c (sparseQR_validate): add new validation test, fix
14 :     -Wall warnings.
15 :     * src/dppMatrix.c,dtrMatrix.c,dgCMatrix.c,dgeMatrix.c,dspMatrix.c:
16 :     Use dup_mMatrix_as_dgeMatrix.
17 :    
18 : bates 1403 2006-08-20 Douglas Bates <bates@R-project.org>
19 :    
20 :     * src/sparseQR.c: Fix thinko in sparseQR_resid_fitted.
21 :     * tests/sparseQR.R: Added
22 :     * man/sparseQR-class.Rd: Document methods for qr.* generics
23 :     * R/sparseQR.R: Return correct # of coefs; fix cut-and-paste errors
24 :    
25 : bates 1398 2006-08-19 Douglas Bates <bates@R-project.org>
26 :    
27 :     * NAMESPACE, R/sparseQR.R, src/init.c,sparseQR.[ch],SOURCES_C.mkf:
28 :     Added methods for sparseQR for qr.qy, qr.qty, qr.coef, qr.resid
29 :     and qr.fitted.
30 :     * src/Mutils.[ch]: Added dup_mMatrix_as_dgeMatrix utility
31 :     * src/dgCMatrix.c: Check for ordering before storing q in dgCMatrix_QR
32 :    
33 : maechler 1389 2006-08-18 Martin Maechler <maechler@stat.math.ethz.ch>
34 :    
35 :     * R/AllGeneric.R: add "qr" and "chol" generics; via 'trick' since
36 :     the base version has no "..." argument.
37 :    
38 :     * R/sparseMatrix.R (prSpMatrix): fix the triangular unit diagonal case.
39 :    
40 :     * R/Matrix.R: define and
41 :     * NAMESPACE: export as.numeric() and as.logical() methods.
42 :     Let's hope these do not badly slow down something...
43 :     Finally export the zapsmall() method.
44 :    
45 : bates 1388 2006-08-17 Douglas Bates <bates@R-project.org>
46 :    
47 :     * src/dgCMatrix.[ch] (dgCMatrix_matrix_solve), src/init.c,
48 :     R/dgCMatrix.R: solve methods for dgCMatrix and dense RHS.
49 :     * src/dtCMatrix.c :Remove code that is no longer used
50 :     * R/dtCMatrix.R: Use C code for diagU2N in CsparseMatrix classes
51 :    
52 : bates 1370 2006-08-14 Douglas Bates <bates@R-project.org>
53 :    
54 : bates 1373 * src/Csparse.[ch],init.c (Csparse_to_logical): Added utilities
55 :     Csparse_to_logical and Csparse_symmetric_to_general.
56 :     * R/dgCMatrix.R,dsCMatrix.R,Csparse.R : Consolidate general
57 : maechler 1389 coercion methods between CsparseMatrix and TsparseMatrix.
58 : bates 1373
59 :     2006-08-14 Douglas Bates <bates@R-project.org>
60 :    
61 : bates 1370 * R/dtCMatrix.R,dgCMatrix.R,Csparse.R src/init.c,dgCMatrix.[ch],
62 :     Csparse.[ch],chm_common.c,dense.c : Use CHOLMOD code and methods
63 :     for CsparseMatrix, TsparseMatrix, denseMatrix or matrix when
64 :     possible.
65 :    
66 : bates 1368 2006-08-12 Douglas Bates <bates@R-project.org>
67 :    
68 :     * src/chm_common.[ch],Csparse.[ch],Tsparse.[ch],CHMfactor.c,dtTMatrix.c,
69 :     dgTMatrix.c,dgCMatrix.c,dsCMatrix.c,dtTMatrix.c, R/dsTMatrix.R,
70 :     Tsparse.R,Csparse.R,dgTMatrix.R,dsCMatrix.R,lsCMatrix.R:
71 :     generalize conversions between TsparseMatrix, CsparseMatrix,
72 :     denseMatrix and matrix. Preserve triangularity property and
73 :     propagate Dimnames in the easy cases.
74 :    
75 : bates 1365 2006-08-10 Douglas Bates <bates@R-project.org>
76 :    
77 :     * src/lmer.c: adjust checks in glmer_init for S4SXP
78 :     * tests/validObj.R: check of all(eq) should be all(eq@x) - worked
79 :     before S4SXP but for the wrong reasons.
80 :    
81 : bates 1354 2006-08-08 Douglas Bates <bates@R-project.org>
82 :    
83 : bates 1360 * src/Csparse.c (Csparse_crossprod): tcrossprod result has stype = -1.
84 :     Later modified to return the upper triangle only.
85 :     * R/dgTMatrix.R: Remove vestigial crossprod and tcrossprod methods.
86 : maechler 1389
87 : bates 1352 2006-08-07 Douglas Bates <bates@R-project.org>
88 :    
89 :     * src/Csparse.c (Csparse_crossprod): Set stype on result to avoid
90 :     R-level conversion to a sparse symmetric class.
91 :     * R/Tsparse.R,R/Csparse.R (crossprod and tcrossprod methods):
92 :     Remove conversion to sparse symmetric classes (now done in C code).
93 :    
94 : maechler 1349 2006-08-07 Martin Maechler <maechler@stat.math.ethz.ch>
95 :    
96 : maechler 1351 * R/dgCMatrix.R: disable old crossprod and tcrossprod methods
97 :     * man/band.Rd: adapt the \dontshow{} unit test.
98 :    
99 :     2006-08-07 Martin Maechler <maechler@stat.math.ethz.ch>
100 :    
101 : maechler 1349 * DESCRIPTION (Version): 0.995-14 for CRAN
102 :    
103 :     * tests/other-pkgs.R: oops: library(Matrix) outside *if* !
104 :    
105 :     * R/sparseMatrix.R (Tsp2grNEL): fixed Tsparse -> graph coercion
106 :     * tests/other-pkgs.R: more checks, sparseMatrix -> graph
107 :    
108 :     * R/Auxiliaries.R (as_Tsparse, as_Rsparse): new
109 :     * R/Tsparse.R (tril, triu, band): methods
110 : bates 1352 * R/dgRMatrix.R (tril, ...): ditto
111 :     * man/band.Rd: ditto
112 : maechler 1349
113 :     2006-08-04 Martin Maechler <maechler@stat.math.ethz.ch>
114 :    
115 :     * R/Matrix.R (head, tail): directly use utils:::head.matrix
116 :     to be up-to-date automatically.
117 :    
118 : maechler 1346 2006-08-03 Martin Maechler <maechler@stat.math.ethz.ch>
119 :    
120 :     * DESCRIPTION (Version): 0.995-13 to be released to CRAN
121 :    
122 :     * DESCRIPTION (Lazydata): no, instead of 'yes' because it fails for:
123 :     * data/CAex.R, inst/external/CAex_slots.rda: replacing data/CAex.rda
124 :     * data/KNex.R, inst/external/KNex_slots.rda: replacing data/KNex.rda
125 :     such that the S4 objects are always created by the current version
126 :     of R and 'Matrix' class definitions.
127 :    
128 : bates 1342 2006-08-01 Douglas Bates <bates@R-project.org>
129 :    
130 :     * R/lmer.R (LMEoptimize method), tests/lmer.R,
131 : maechler 1346 inst/external/test3comp.rda: Added warnings for convergence on
132 : bates 1342 boundary and test cases.
133 :    
134 :     * src/lmer.c (mer_postVar): Modified to return the variances that
135 :     are marginal to the fixed effects, not conditional on them (which
136 :     is what the bVar slot contents represent).
137 :    
138 : bates 1338 2006-07-31 Douglas Bates <bates@R-project.org>
139 :    
140 :     * NAMESPACE, src/lmer.c, R/lmer.R (hatTrace): Add the hatTrace
141 :     function which calls the C function mer_hat_trace2.
142 : maechler 1346
143 : bates 1342 * man/ranef.Rd: Include description of "postVar" argument and
144 :     producing a caterpillar plot.
145 : bates 1338
146 : maechler 1335 2006-07-31 Martin Maechler <maechler@stat.math.ethz.ch>
147 :    
148 :     * NAMESPACE: change "correlation" to "corMatrix"
149 :     * R/AllClass.R: to avoid clash with S3 class in 'nlme'.
150 : bates 1352 * R/dpoMatrix.R: ditto
151 :     * R/lmer.R: ditto
152 : maechler 1335
153 : bates 1338 2006-07-28 Douglas Bates <bates@R-project.org>
154 :    
155 :     * src/lmer.c (internal_mer_RZXinv): Split the calculation of the
156 :     RZXinv slot's contents into a separate internal function that can
157 :     be used in mer_hat_trace.
158 :    
159 : maechler 1331 2006-07-22 Martin Maechler <maechler@stat.math.ethz.ch>
160 :    
161 :     * R/Matrix.R: Coercions "Matrix" -> (sparse|dense)Matrix
162 :     via new smart
163 :     * R/Auxiliaries.R (as_Csparse, as_dense, .M.shapse): new
164 :     utility functions.
165 :    
166 :    
167 : maechler 1330 2006-07-21 Martin Maechler <maechler@stat.math.ethz.ch>
168 :    
169 : maechler 1331 * R/Csparse.R (tril, triu, band): do return *triangular* classed
170 :     matrices when appropriate; band() even symmetric ones.
171 :     (replCmat): extend to potentially all "CsparseMatrix"
172 :     * R/Tsparse.R (replTmat): extend to all "TsparseMatrix"; hence
173 :     allow subassignment for special sparse matrices.
174 :    
175 :     * R/Auxiliaries.R (as_geClass): factor out the .M.kind() functionality
176 :    
177 : maechler 1330 * src/lmer.c (mer_MCMCsamp, glmer_MCMCsamp): new 'verbose'
178 :     argument; in glmer_*(): print only if(verbose).
179 :    
180 :     speed-optimize a few places by moving REAL(.) out of loops.
181 :    
182 :     * src/lmer.h, src/init.h, R/lmer.R: related to above.
183 :    
184 : maechler 1329 2006-07-20 Martin Maechler <maechler@stat.math.ethz.ch>
185 :    
186 :     * R/Matrix.R("["): disable ("Matrix", i = "logical", j = "missing"),
187 :     since that wrongly triggers also for M[ logi , ]
188 :    
189 :     * R/denseMatrix.R: "[" methods now also work e.g. when indexing
190 :     a symmetric matrix that results in a non-symmetric one.
191 :     * R/Auxiliaries.R (as_geClass): new function used in "[" above.
192 :    
193 :     * R/dMatrix.R: make round(M) work as round(M, 0)
194 :    
195 :     * R/dgTMatrix.R (image): coordinate system and axis now use
196 :     1-based indices, not 0-based ones.
197 :    
198 :     * R/Tsparse.R (.ind.prep for "["): get rid of max(<empty>) warning.
199 :     * tests/indexing.R: test it.
200 :    
201 :     * NAMESPACE: export isSymmetric(); has been a generic in "base" for a while;
202 :     * man/isSymmetric-methods.Rd: and document it.
203 :    
204 :     * R/SparseM-conv.R: added coercion methods for some 'SparseM' matrices.
205 :     * man/SparseM-conv.Rd: docu them
206 :    
207 :     * tests/other-pkgs.R: renamed from tests/graph.R and add example
208 :     for 'SparseM' conversions
209 :    
210 :     2006-07-17 Douglas Bates <Douglas.Bates@R-project.org>
211 :    
212 :     * R/Matrix.R (head): added head() and tail() methods.
213 :    
214 :     2006-07-17 Martin Maechler <maechler@stat.math.ethz.ch>
215 :    
216 :     * DESCRIPTION (Version): 0.995-12 released to CRAN
217 :    
218 : maechler 1319 2006-07-15 Martin Maechler <maechler@stat.math.ethz.ch>
219 :    
220 :     * tests/simple.R: add check for correct dsT -> dgT coercion;
221 :     add check for correct printing of symmetric sparse matrices.
222 :    
223 :     * R/Auxiliaries.R (non0ind): return *all* non-0 entry indices also
224 :     for sparse symmetric matrices.
225 :    
226 :     * src/dsTMatrix.c (dsTMatrix_as_dgTMatrix): do not copy the
227 :     diagonal twice.
228 :    
229 : bates 1316 2006-07-11 Douglas Bates <Douglas.Bates@R-project.org>
230 :    
231 :     * src/dsTMatrix.c (dsTMatrix_as_dgTMatrix): Fix a case of INTEGER
232 : maechler 1319 being applied to the x slot (detected by Brian Ripley).
233 : bates 1316
234 : maechler 1315 2006-07-10 Martin Maechler <maechler@stat.math.ethz.ch>
235 :    
236 :     * src/dgCMatrix.c (dgCMatrix_validate): 'p' slot must have correct length.
237 :    
238 :     * R/Auxiliaries.R (isTriC): fix buglet (we were 1-based!)
239 :    
240 :     2006-07-08 Martin Maechler <maechler@stat.math.ethz.ch>
241 :    
242 :     * src/lgCMatrix.c (lgCMatrix_diag): new function
243 :     * R/lgCMatrix.R (diag): for new method
244 :    
245 :     * R/AllClass.R (TsparseMatrix): do use Tsparse_validate
246 :     ==> construction of illegal "*gTMatrix" via new() should
247 :     now be much less easy:
248 :     * tests/Class+Meth.R: assertError() for some illegal "dgT*"
249 :    
250 :     * R/Matrix.R (Matrix): Matrix(0, nrow,ncol) now "goes sparse"
251 :     directly.
252 :     * man/Matrix.Rd: documents it.
253 :    
254 : bates 1311 2006-07-06 Douglas Bates <bates@R-project.org>
255 :    
256 :     * src/pedigree.c (pedigree_inbreeding): Correction in
257 :     initialization. This function is not currently being used and is
258 :     not fully tested.
259 :    
260 : bates 1312 * NAMESPACE, R/{AllClass.R,lmer.R}, src/{init.c,lmer.c}:
261 :     Introduced the glmer class. Added code for mcmcmsamp on glmer
262 :     objects. Modified validity check on pedigree objects to account
263 :     for nonparallel patterns of missingness of parents.
264 : bates 1311
265 : bates 1313 * man/{lmer-class.Rd,mcmcsamp.Rd}: Update documentation for glmer
266 :     class.
267 : maechler 1315
268 :     2006-07-01 Martin Maechler <maechler@stat.math.ethz.ch>
269 :    
270 :     * R/pMatrix.R: coercion pMatrix -> Tsparse
271 :    
272 : bates 1300 2006-06-12 Douglas Bates <bates@R-project.org>
273 :    
274 : maechler 1319 * DESCRIPTION (Version): 0.995-11 released to CRAN
275 :    
276 : bates 1300 * R/lmer.R (mcmcsamp method): Corrected arrangments of names on
277 :     the output from mcmcsamp.
278 :    
279 : bates 1298 2006-06-10 Douglas Bates <bates@R-project.org>
280 :    
281 : bates 1300 * R/lmer.R (simulestimate): added C code for calculating the trace
282 :     of the hat matrix.
283 : bates 1298
284 : maechler 1295 2006-06-09 Martin Maechler <maechler@stat.math.ethz.ch>
285 :    
286 :     * R/diagMatrix.R (setAs): define coercion methods to sparse matrix
287 :     classes.
288 : maechler 1315 * R/sparseMatrix.R etc: multiplication of diagonal and sparse
289 : maechler 1295
290 : maechler 1290 2006-06-08 Martin Maechler <maechler@stat.math.ethz.ch>
291 :    
292 :     * R/dgTMatrix.R (colSums): etc. All four of
293 :     colSums(), rowSums(), colMeans(), rowMeans() now should work for
294 :     all "Matrices".
295 :    
296 : bates 1288 2006-06-01 Douglas Bates <bates@stat.wisc.edu>
297 :    
298 :     * R/lmer.R (panel.ci): Add a reference line at zero and a
299 :     background grid to the qqmath plot of ranef.lmer.
300 :    
301 : bates 1287 2006-05-30 Douglas Bates <bates@stat.wisc.edu>
302 : bates 1284
303 : bates 1287 * R/lmer.R (expandSlash): Functions (non-exported) to allow nested
304 :     grouping factors to be specified in the formula as (1|foo/bar).
305 :    
306 :     2006-05-27 Douglas Bates <bates@stat.wisc.edu>
307 :    
308 : bates 1284 * R/lmer.R (findbars and others): Change check of is.numeric to
309 :     !is.language to resolve the bug reported by Jacob Wegelin.
310 :    
311 :     * src/pedigree.c (pedigree_inbreeding): Initial implementation of
312 :     code to evaluate inbreeding coefficients without calculating T,
313 :     based on code in Sargolzaei and Iwaisaki's paper.
314 :    
315 : bates 1283 2006-05-27 Douglas Bates <bates@stat.wisc.edu>
316 :    
317 :     * R/{lmer.R,AllGeneric.R}, src/{init.c,lmer.[ch]}: Added local
318 :     generic and mer methods for isNested and denomDF. This denomDF was
319 :     an attempt to emulate that in lme but I don't think that makes
320 :     sense. Use the trace of the hat matrix instead.
321 :    
322 : maechler 1271 2006-05-17 Martin Maechler <maechler@stat.math.ethz.ch>
323 :    
324 :     * R/sparseMatrix.R: Matrix <-> graph methods: can no longer use
325 :     the C code depending on a slot structure that's no longer valid.
326 : bates 1352 * src/dgTMatrix.c: ditto (also: src/init.c src/dgTMatrix.h)
327 : maechler 1271
328 :    
329 : bates 1268 2006-05-17 Douglas Bates <bates@stat.wisc.edu>
330 :    
331 :     * R/{AllGeneric.R,Csparse.R},man/band.Rd,NAMESPACE: changed name
332 :     of lowerTriMatrix generic and methods to tril (also upper to triu)
333 :     and added a general band extractor.
334 :    
335 : bates 1267 2006-05-16 Douglas Bates <bates@stat.wisc.edu>
336 :    
337 :     * R/pedigree.R (pedigree): Replace sire and dam values outside the
338 :     allowable range with NAs. Added a corresponding check in the
339 :     validity check for the pedigree class.
340 :    
341 :     * R/[CT]sparse.R ([t]crossprod): The result of single-argument
342 :     crossprod methods now inherits from symmetricMatrix.
343 :    
344 : bates 1265 2006-05-15 Douglas Bates <bates@stat.wisc.edu>
345 :    
346 :     * R/AllGeneric.R (lowerTriMatrix): Added (but did not export)
347 :     generics lowerTriMatrix and upperTriMatrix along with methods for
348 :     the Csparse virtual class. Also added a C function Csparse_band
349 :     that implements these methods by calling cholmod_band.
350 :    
351 : maechler 1264 2006-05-15 Martin Maechler <maechler@stat.math.ethz.ch>
352 :    
353 :     * R/Tsparse.R ("["): column or row subsetting; @Dimnames[k] got
354 :     erased when it was NULL. This led to invalid subselections!
355 :    
356 : bates 1259 2006-04-25 Douglas Bates <bates@stat.wisc.edu>
357 :    
358 :     * R/dtCMatrix.R: avoid coercion of dtCMatrix object to dgCMatrix
359 :     in method for "t" so as not to lose the unit diagonal property.
360 :    
361 : bates 1257 2006-04-19 Douglas Bates <bates@stat.wisc.edu>
362 :    
363 :     * R/lmer.R, R/AllGeneric.R, NAMESPACE: Remove the postVar generic
364 :     and methods. This is now an option to the ranef method for the
365 :     mer class.
366 :    
367 :     * src/cs_utils.c: Ensure that the nz component is -1 for a
368 :     compressed column-oriented matrix. Minor formatting cleanup.
369 :    
370 :     * man/lmer-class.Rd: Document the qqmath method for ranef.lmer
371 :     objects.
372 :    
373 : maechler 1253 2006-04-19 Martin Maechler <maechler@stat.math.ethz.ch>
374 :    
375 :     * R/Auxiliaries.R (diagU2N): new for the solve() methods in
376 :     * R/dtCMatrix.R: where dgC -> dgT coercion now preserves diag = "U".
377 :    
378 : bates 1251 2006-04-15 Douglas Bates <bates@stat.wisc.edu>
379 :    
380 :     * src/cs.[ch],src/cs_utils.[ch] : Added Tim Davis' CSparse library
381 :     in cs.[ch] and utilities to interface to that code in cs_utils.[ch].
382 :    
383 :     * R/dtCMatrix.R, src/dtCMatrix.[ch] : CSparse-based solve methods
384 :     for the dtCMatrix class.
385 : maechler 1253
386 : bates 1247 2006-04-12 Douglas Bates <bates@stat.wisc.edu>
387 :    
388 :     * R/pedigree.R, R/AllClass.R, NAMESPACE: added a pedigree class
389 :     and methods for it.
390 :    
391 : maechler 1245 2006-04-12 Martin Maechler <maechler@stat.math.ethz.ch>
392 :    
393 :     * R/dgCMatrix.R: add storage.mode(.) <- "double" for "matrix"
394 :     arguments, such that M %*% 1:6 now works
395 :     * Tests/matprod.R: test the above
396 :    
397 : bates 1244 2006-04-03 Douglas Bates <bates@stat.wisc.edu>
398 : bates 1243
399 :     * R/lmer.R (qqmath,ranef.lmer-method): added a qqmath method for
400 :     the ranef.lmer class.
401 :    
402 :     * R/AllClass.R, NAMESPACE, R/lmer.R: Added a postVar generic and
403 :     methods to extract the posterior variances from the bVar slot.
404 :    
405 : maechler 1238 2006-03-30 Martin Maechler <maechler@stat.math.ethz.ch>
406 :    
407 :     * R/dtCMatrix.R: allow coercion from dgC* to triangular (dtC*)
408 :     * R/dsCMatrix.R: and symmetric (dsC*) 'Csparse' matrices.
409 :    
410 :     * R/Tsparse.R: Tsparse* -> Csparse* coercion now works and is tested in
411 :     * tests/simple: (extended)
412 :    
413 :     * R/sparseMatrix.R (isTriangular): now using much improved
414 :     * R/Auxiliaries.R (isTriC): new triangularity check for *CMatrix
415 :    
416 : bates 1236 2006-03-23 Douglas Bates <bates@stat.wisc.edu>
417 :    
418 :     * src/dsyMatrix.c (dsyMatrix_as_dspMatrix): Propagate DimNames
419 :     (problem report from Franklin Parlamis). This should be done
420 : maechler 1238 generally.
421 : bates 1236
422 : bates 1234 2006-03-21 Douglas Bates <bates@stat.wisc.edu>
423 :    
424 :     * R/AllClass.R,lmer.R: Change the name of the lmer.ranef class to
425 :     ranef.lmer (like summary.lmer). Add the coef.lmer class and
426 :     update the plot methods.
427 :    
428 : bates 1232 2006-03-20 Douglas Bates <bates@stat.wisc.edu>
429 :    
430 :     * R/lmer.R (resid and ranef methods): Added methods for the
431 :     "residuals" and "resid" generic but only for linear mixed model
432 :     fits. Changed the ranef method to return a list of data frames so
433 :     that the plot methods now work.
434 :    
435 : bates 1230 2006-03-16 Douglas Bates <bates@bates2>
436 :    
437 :     * src/dpoMatrix.c (dpoMatrix_chol): Require n > 0 in call to
438 :     dpotrf - otherwise the BLAS on Mac OS X complains and quits.
439 :    
440 :     * DESCRIPTION (Date): New release
441 :    
442 : maechler 1228 2006-03-15 Martin Maechler <maechler@stat.math.ethz.ch>
443 :    
444 :     * DESCRIPTION (Version): 0.995-6 -- to be released to CRAN
445 :    
446 :     * data/KNex.rda: replacing 'mm' and 'y' by KNex <- list(mm=mm, y=y)
447 :     * man/KNex.Rd: and other help files
448 :     * tests/*.R: several ones needed adaption
449 : bates 1352 * inst/doc/Comparisons.Rnw: ditto
450 : maechler 1228
451 : maechler 1226 2006-03-11 Martin Maechler <maechler@stat.math.ethz.ch>
452 :    
453 :     * R/dgCMatrix.R (replCmat): "[<-" methods for dgCMatrix
454 :    
455 :     * tests/indexing.R: tests for new [<- methods for sparse matrices.
456 :    
457 :     2006-03-10 Martin Maechler <maechler@stat.math.ethz.ch>
458 :    
459 :     * R/dgTMatrix.R (replTmat): "[<-" methods for dgTMatrix
460 :    
461 :     * R/Tsparse.R (.ind.prep): fix out-of-range indexing
462 :    
463 :     2006-03-08 Martin Maechler <maechler@stat.math.ethz.ch>
464 :    
465 :     * R/dMatrix.R: enable things like M [ M < 10 ]
466 :     * R/dgeMatrix.R: implement it
467 :    
468 : maechler 1222 2006-03-06 Martin Maechler <maechler@stat.math.ethz.ch>
469 :    
470 :     * R/AllClass.R: define "summary.mer" and "*.lmer"
471 :     * R/lmer.R (summary): summary(<mer>) computes & returns the above;
472 :     * R/lmer.R (show): now works with summary()
473 :    
474 :     2006-03-04 Martin Maechler <maechler@stat.math.ethz.ch>
475 :    
476 :     * R/dgCMatrix.R: finally direct "Arith" dgC o dgC
477 :     * R/Auxiliaries.R (WhichintersectInd): and other utilities to
478 :     support the above
479 :    
480 : bates 1213 2006-02-07 Douglas Bates <bates@stat.wisc.edu>
481 :    
482 :     * R/lmer.R (lmer): fix initial values of offset and weights for glm.fit.
483 :     Use glmFit$prior.weights for weights in a glmm.
484 :     Allow an option usePQL = FALSE to skip the PQL steps for the
485 :     Laplace method (and, in time, the AGQ method).
486 :    
487 :     * src/lmer.c (mer_factor): Move downdating and factoring of XtX
488 :     into a separate function internal_mer_Xfactor to be able to call
489 :     it from internal_bhat.
490 :    
491 : maechler 1200 2006-01-23 Martin Maechler <maechler@stat.math.ethz.ch>
492 :    
493 :     * tests/Class+Meth.R (tstMatrixClass): function for much better
494 :     testing; now again of all actual classes.
495 :    
496 :     * src/Mutils.c (MAKE_TRIANGULAR_BODY, MAKE_SYMMETRIC_BODY):
497 :     use macros and define make_d_matrix_* and make_i_matrix_*
498 :     where _i_ is for the ldense routines:
499 :    
500 :     * src/ldense.c (ltrMatrix_as_lgeMatrix): provide functions
501 :     * src/ldense.c (lsyMatrix_as_lgeMatrix):
502 :    
503 :     * R/ldenseMatrix.R: use the above in setAs(*,"lgeMatrix")
504 :    
505 :    
506 : maechler 1174 2006-01-16 Martin Maechler <maechler@stat.math.ethz.ch>
507 :    
508 :     * R/Matrix.R (Matrix): has become much "smarter" now auto-producing
509 :     many different kinds of matrices.
510 :     * R/*.R: quite a few new methods were needed for R CMD check with
511 :     new Matrix(). Very good for users playing around.
512 :    
513 :    
514 : maechler 1165 2006-01-15 Martin Maechler <maechler@stat.math.ethz.ch>
515 :    
516 :     * src/dgeMatrix.c (dMatrix_validate): new
517 :     * src/Mutils.c (dense_nonpacked_validate): new
518 :    
519 :     * src/dtrMatrix.c (dtrMatrix_validate): improved/fixed
520 :    
521 :    
522 :     2006-01-14 Douglas Bates <bates@stat.wisc.edu>
523 :    
524 :     * R/AllClass.R (compMatrix), (generalMatrix): new virtual classes
525 :    
526 : bates 1123 2006-01-07 Douglas Bates <bates@stat.wisc.edu>
527 : bates 1119
528 : maechler 1127 * DESCRIPTION (Version): 0.99-6 released to CRAN
529 :    
530 : bates 1119 * src/dgBCMatrix.c (cscb_trcbsm): Fix due to Peter Dalgaard for
531 :     segfault in cases with multiple non-nested grouping factors.
532 :    
533 : maechler 1109 2006-01-03 Martin Maechler <maechler@stat.math.ethz.ch>
534 :    
535 :     * DESCRIPTION (Version): 0.99-4 to be released to CRAN
536 :     (Depends): also on 'utils'
537 :    
538 :     * R/AllClass.R (diagonalMatrix): new class with "ddi*" and "ldi*"
539 :     * R/diagMatrix.R (Diagonal): constructor and methods for
540 :     diagonal matrices
541 :    
542 :     * R/ltTMatrix.R: new "minimal methods"
543 :    
544 : maechler 1091 2005-12-12 Martin Maechler <maechler@stat.math.ethz.ch>
545 :    
546 :     * R/AllGeneric.R (tcrossprod): 2-argument version; here, and for
547 :     all methods (and help files).
548 :    
549 : maechler 1084 2005-12-09 Martin Maechler <maechler@stat.math.ethz.ch>
550 :    
551 :     * R/Auxiliaries.R (dimNamesCheck): fixed thinko -> bug
552 :     for case (dimn. op no_dimn.)
553 :    
554 :     2005-11-14 Douglas Bates <bates@stat.wisc.edu>
555 :    
556 : maechler 1174 * DESCRIPTION (Version): 0.99-2 released to CRAN
557 : maechler 1084
558 : bates 988 2005-10-21 Douglas Bates <bates@stat.wisc.edu>
559 :    
560 :     * R/lmer.R (simulate method): Fixed a drop=FALSE problem reported
561 :     by Julian Faraway.
562 :    
563 : maechler 976 2005-10-06 Martin Maechler <maechler@stat.math.ethz.ch>
564 :    
565 :     * R/Auxiliaries.R (try_as): new utility
566 :     * R/sparseMatrix.R: use try_as() in coercion to original class
567 :    
568 : maechler 956 2005-09-30 Martin Maechler <maechler@stat.math.ethz.ch>
569 :    
570 :     * src/dgCMatrix.c (double_to_csc): and dgeMatrix_to_csc()
571 :    
572 :     2005-09-29 Martin Maechler <maechler@stat.math.ethz.ch>
573 :    
574 :     * R/Auxiliaries.R (dimNamesCheck): added
575 :    
576 :     * R/Matrix.R (as.array), (as.vector): new
577 :    
578 : maechler 954 2005-09-28 Martin Maechler <maechler@stat.math.ethz.ch>
579 :    
580 :     * R/Matrix.R (Matrix): get logical argument 'sparse' with a smart
581 : maechler 956 default.
582 :     * R/AllClass.R: move 'factors' slot toplevel "Matrix";
583 :     "pMatrix" now contains "sparseMatrix"
584 : maechler 954
585 : maechler 948 2005-09-26 Martin Maechler <maechler@stat.math.ethz.ch>
586 :    
587 :     * tests/Class+Meth.R: new tests; t(t(m)) == m
588 :    
589 :     * src/dtCMatrix.c (tsc_transpose): add forgotten "diag" slot
590 :    
591 :     * src/dsTMatrix.c (dsTMatrix_as_dsCMatrix): bad typo (segfault!)
592 :     * src/dtTMatrix.c (dtTMatrix_as_dtCMatrix): new
593 :    
594 :     * R/dspMatrix.R: typo in "t" method
595 :    
596 : maechler 925 2005-09-18 Douglas Bates <bates@wisc.edu>
597 :    
598 :     * R/AllClass.R (TsparseMatrix), CsparseM* and RsparseM*
599 :     * R/Tsparse.R: instead of R/gTMatrix.R
600 :     * R/Csparse.R: new
601 :     * src/Tsparse.c (Tsparse_to_Csparse): new; -> cholmod_()
602 :     * src/Tsparse.c: new; many trivial methods calling cholmod_()
603 :     * src/Csparse.c (Csparse_to_Tsparse), transpose, (mat|cross)prod:
604 :     via cholmod
605 :    
606 :     2005-09-16 Martin Maechler <maechler@stat.math.ethz.ch>
607 :    
608 :     * R/Auxiliaries.R (non0ind): new function using new C code
609 :     * src/dgCMatrix.c (compressed_non_0_ij): new utility
610 :    
611 : bates 917 2005-09-15 Douglas Bates <bates@localhost.localdomain>
612 :    
613 :     * src/chm_common.h: header file required by all C sources that
614 : maechler 1174 call CHOLMOD functions. It defines a cholmod_common structure
615 : bates 917 called 'c' whose address is passed as the last argument to
616 :     (virtually) every CHOLMOD function.
617 :    
618 :     * src/Pattern.c: Simple example of the use of CHOLMOD.
619 :    
620 :     * src/init.c: initialize and finalize the cholmod_common structure.
621 :    
622 :     * src/Makefile: Added source packages CHOLMOD UMFPACK AMD COLAMD
623 :     LDL and CCOLAMD from the U. of Florida sparse matrix library.
624 :    
625 : maechler 908 2005-09-08 Martin Maechler <maechler@stat.math.ethz.ch>
626 :    
627 :     * inst/test-tools.R: new file collecting the utility functions used
628 :     in ./tests/*.R
629 :    
630 :     * R/ddenseMatrix.R (cbind2): new methods for "numeric" and "matrix"
631 :     * R/Matrix.R (cbind2): methods for NULL and missing
632 :    
633 : maechler 886 2005-08-31 Martin Maechler <maechler@stat.math.ethz.ch>
634 :    
635 :     * R/AllClass.R: new "index" class for "[" and "[<-":
636 :     First cut at "symmetricMatrix" and "triangularMatrix"
637 :     * R/gTMatrix.R (.ind.prep): new function;
638 : maechler 1174 Logical and character indexing now work too.
639 : maechler 886 * R/Matrix.R: cheap "[<-" methods for denseMatrix now work
640 :     * tests/indexing.R: new, including *.Rout.save
641 :     * tests/dgTMatrix.R: new
642 :    
643 : bates 876 2005-08-29 Douglas Bates <bates@wisc.edu>
644 :    
645 :     * src/dgTMatrix.c (graphNEL_as_dgTMatrix): Corrected the position
646 :     indicator pos not being updated. Also enforced upper triangular
647 :     for symmetric case. Need to coerce edges component of elements of
648 :     edge list - grr! (Why don't they define their classes cleanly?)
649 :    
650 : maechler 871 2005-08-26 Martin Maechler <maechler@stat.math.ethz.ch>
651 :    
652 :     * R/Matrix.R: added first "[<-" methods; not yet functional
653 : bates 1352 * R/denseMatrix.R: ditto
654 : maechler 871 * man/Subassign-methods.Rd: new help file for these
655 :    
656 :     2005-08-25 Martin Maechler <maechler@stat.math.ethz.ch>
657 :    
658 :     * DESCRIPTION (Version): 0.98-6
659 :    
660 :     * R/denseMatrix.R: new file for "[" fallback methods for all dense
661 :     matrices.
662 :    
663 : maechler 868 2005-08-19 Martin Maechler <maechler@stat.math.ethz.ch>
664 :    
665 :     * src/lgCMatrix.c (lcsc_to_matrix): new; need for
666 :     as( <logical>, "matrix")
667 :    
668 :     * R/pMatrix.R: coercion to "lgTMatrix"
669 :    
670 :     * R/gTMatrix.R: new virtual class to define "[" methods for.
671 :     * man/gTMatrix-class.Rd:
672 :     * General slight re-organization of where "[" methods are defined.
673 :     more to come.
674 :    
675 : maechler 871 2005-08-18 Douglas Bates <bates@wisc.edu>
676 : maechler 868
677 : maechler 1174 * DESCRIPTION (Version): 0.98-5 released to CRAN
678 : maechler 871
679 :     * src/dgTMatrix.c (graphNEL_as_dgTMatrix): add first graphNEL methods
680 :     * .....
681 :    
682 : bates 863 2005-08-18 Douglas Bates <bates@localhost.localdomain>
683 :    
684 :     * R/lmer.R: Corrected naming scheme in mcmcsamp to work with lmer
685 :     or glmer objects.
686 :    
687 : maechler 860 2005-08-17 Martin Maechler <maechler@stat.math.ethz.ch>
688 :    
689 :     * DESCRIPTION (Version): 0.98-4 : upload to CRAN
690 :    
691 :     2005-08-16 Douglas Bates <bates@localhost.localdomain>
692 :    
693 :     * R/HBMM.R: finish re-writing R-only code.
694 :    
695 : bates 854 2005-08-15 Douglas Bates <bates@localhost.localdomain>
696 :    
697 :     * man/externalFormats.Rd: move documentation for writeHB and
698 :     writeMM here.
699 :    
700 :     * src/mmio.c: replace inclusion of <malloc.h> by <stdlib.h>
701 :     (suggested by Paul Roecker).
702 :    
703 :     * tests/validObj.R (assertError): Comment out test that is failing
704 :     after recent changes in r-devel.
705 :    
706 : maechler 860
707 : maechler 848 2005-08-11 Martin Maechler <maechler@stat.math.ethz.ch>
708 :    
709 :     * R/AllClass.R: intermediate virtual class "denseMatrix"
710 :     * man/denseMatrix-class.Rd
711 :     * NAMESPACE: export it, and also export
712 :     * man/unused-classes.Rd: "iMatrix", "zMatrix" and "ldenseMatrix"
713 :    
714 : bates 846 2005-08-10 Douglas Bates <bates@wisc.edu>
715 :    
716 : maechler 848 * DESCRIPTION (Version): 0.98-3 to CRAN
717 :    
718 : bates 846 * src/dtrMatrix.c (dtrMatrix_validate): fixed up validation and
719 :     matrix_solve code (which was really, really wrong).
720 :    
721 : bates 835 2005-08-07 Douglas Bates <bates@wisc.edu>
722 : maechler 834
723 :     * DESCRIPTION (Version): 0.98-2
724 :    
725 :     * R/HBMM.R (readHB), (readMM): read Matrix Market formats
726 :    
727 :     * R/lmer.R (abbrvNms): new
728 :     * R/lmer.R (mcmcsamp): allow transformed parameters
729 : bates 835 * src/HBMM.c (Matrix_writeMatrixMarket): Added read/write routines
730 :     for the Harwell-Boeing and the MatrixMarket formats.
731 : maechler 834
732 :     2005-08-04 Martin Maechler <maechler@stat.math.ethz.ch>
733 :    
734 :     * man/dtrMatrix-class.Rd: add examples
735 : bates 835 * man/dtpMatrix-class.Rd: ditto; plus note about PROBLEM
736 : maechler 834
737 :     * TODO: note the dtpMatrix (docu) bug
738 :    
739 :     * R/zzz.R (.onLoad): assignInNamespace("as.matrix", *, "base")
740 :     in order to ensure that new as.matrix() is used by old functions,
741 :     e.g., svd(), qr(), eigen(), dist(),..;
742 :     apply(), also matplot() or pairs().
743 :    
744 :    
745 :     2005-08-03 Martin Maechler <maechler@stat.math.ethz.ch>
746 :    
747 :     * R/lmer.R: add 'fixme' comments and move the linear vs glm check;
748 :     add comments about 'control' / lmerControl() arguments
749 :    
750 : bates 835 2005-07-27 Douglas Bates <bates@wisc.edu>
751 : bates 820
752 : bates 835 * man/sleepstudy.Rd: Added the sleep data set.
753 : maechler 1174 * DESCRIPTION (Version): 0.98-1 released to CRAN
754 : bates 820
755 : bates 835 2005-07-12 Douglas Bates <bates@wisc.edu>
756 : maechler 834 * man/sleepstudy.Rd: Added the sleep data set.
757 :    
758 : bates 809 * R/lmer.R (glmmMCMC): Added PACKAGE = "Matrix" in a couple of
759 :     .Call calls that were producing spurious output.
760 :    
761 : bates 835 2005-07-05 Douglas Bates <bates@wisc.edu>
762 : bates 801
763 :     * R/lmer.R (lmer): stored updated variance component estimates in
764 :     mer object for the generalized model. (Bug reported by Renaud
765 :     Lancelot).
766 :    
767 : bates 835 2005-07-03 Douglas Bates <bates@wisc.edu>
768 : bates 794
769 :     * src/lmer.c (glmer_devAGQ): Added AGQ for single grouping factor,
770 :     unidimensional case.
771 :    
772 : bates 835 2005-06-08 Douglas Bates <bates@wisc.edu>
773 : maechler 791
774 :     * DESCRIPTION (Version): 0.96-1
775 :    
776 : maechler 1174 * moved lmer-class' R and C code moved from lme4 to here
777 : maechler 791
778 : bates 835 2005-06-04 Douglas Bates <bates@wisc.edu>
779 : bates 763
780 :     * R/dgCMatrix.R: Call to csc_matrix_mm used undefined arguments
781 :     (reported by Guissepe Ragusa <gragusa@ucsd.edu>)
782 :    
783 : bates 835 2005-06-02 Douglas Bates <bates@wisc.edu>
784 : bates 763
785 :     * src/Makefile.win: Forgot to update this when Makefile changed.
786 :    
787 : bates 835 2005-05-11 Douglas Bates <bates@wisc.edu>
788 : bates 726
789 :     * src/dgCMatrix.c (csc_transpose): Simplified function fixing a
790 :     bug reported by Kurt Hornik and Michael Hahsler.
791 :    
792 : bates 835 2005-05-10 Douglas Bates <bates@wisc.edu>
793 : bates 725
794 :     * src/lgCMatrix.c (Matrix_lgClgCmm): Implementation of methods for
795 :     logical sparse matrices. These will also be used in the symbolic
796 :     analysis for lmer objects.
797 :    
798 :     * src/dsCMatrix.c (dsCMatrix_matrix_solve): Copied the dimensions
799 :     of b to the result. Fixes bug reported by Jean.Coursol@math.u-psud.fr
800 : maechler 791
801 : bates 835 2005-05-06 Douglas Bates <bates@wisc.edu>
802 : bates 714
803 :     * src/dgeMatrix.c (dgeMatrix_colsums): Added an implementation of
804 :     colMeans, colSums, rowMeans and rowSums.
805 :    
806 : bates 835 2005-04-18 Douglas Bates <bates@wisc.edu>
807 : bates 692
808 :     * src/lgCMatrix.[ch]: code for _validate method and stub for
809 :     multiplication operation.
810 :    
811 :     * src/dgeMatrix.c (dgeMatrix_matrix_solve): Passing wrong argument
812 :     to dgetrs.
813 :    
814 :     * src/init.c: Fix cut-and-paste error in definition of
815 :     dgeMatrix_matrix_solve
816 :    
817 :     * src/{many files}: Tighten code by using ALLOC_SLOT.
818 :    
819 : bates 835 2005-04-15 Douglas Bates <bates@wisc.edu>
820 : bates 692
821 :     * R/AllClass.R: Add lgTMatrix and lgCMatrix classes
822 :    
823 :     * DESCRIPTION: Eliminate import of stats.
824 :    
825 : maechler 791
826 : bates 835 2005-04-06 Douglas Bates <bates@wisc.edu>
827 : bates 692
828 :     * R/AllClass.R : add logical sparse matrix classes
829 :    
830 : maechler 687 2005-04-01 Martin Maechler <maechler@stat.math.ethz.ch>
831 :    
832 :     * R/dgTMatrix.R: add "[" method for triplet matrices
833 :     * R/sparseMatrix.R: and other sparse ones; --> add show() for sparse
834 :    
835 : bates 835 2005-03-31 Douglas Bates <bates@wisc.edu>
836 : maechler 687
837 :     * DESCRIPTION (Version): release 0.95-5 to CRAN
838 :    
839 :     * R/dMatrix.R: add %*%, crossprod and solve "fallback" methods
840 :     * R/sparseMatrix.R: %*%, crossprod()
841 :     * R/dgeMatrix.R: more "fallback" methods for numeric/dense matrices
842 :     * man/*.Rd: move method definitions to 'Matrix' and 'dMatrix'
843 :     * src/lmer.c (lmer_fitted): fix thinko
844 :    
845 : maechler 676 2005-03-26 Martin Maechler <maechler@stat.math.ethz.ch>
846 :    
847 :     * R/AllClass.R: add two virtual sparse classes ``on top''
848 :    
849 :     2005-03-24 Martin Maechler <maechler@stat.math.ethz.ch>
850 :    
851 :     * R/AllClass.R (setClass): use "VIRTUAL" for the virtual classes;
852 :     correspondingly fix examples and tests/ since new()
853 :     doesn't work for virtual classes.
854 :    
855 : maechler 658 2005-03-17 Martin Maechler <maechler@stat.math.ethz.ch>
856 :    
857 :     * R/Matrix.R (as.matrix): method and one for unname()
858 :     * tests/dpoMatrix.R: tests should now be less platform dependent;
859 :     also run for R 2.1.0; using as.matrix()
860 :    
861 : bates 835 2005-03-15 Douglas Bates <bates@wisc.edu>
862 : maechler 658
863 :     * R/pMatrix.R: "pMatrix" class added
864 :     * ....
865 :    
866 : bates 835 2005-03-14 Douglas Bates <bates@wisc.edu>
867 : bates 645
868 :     * R/dtpMatrix.R: Add unpack method and an example.
869 :    
870 :     * src/dsyMatrix.c (dsyMatrix_trf): Add BunchKaufman factorization
871 :     of general symmetric matrices and associated S4 methods.
872 :    
873 : maechler 658 2005-03-10 Martin Maechler <maechler@stat.math.ethz.ch>
874 :     +
875 :     2005-03-05 Martin Maechler <maechler@stat.math.ethz.ch>
876 :    
877 :     * R/dgeMatrix.R (setAs): and many other files: more coercion,
878 :     crossprod() and "%*%" methods added; tests, too.
879 :     * tests/matprod.R: new, for testing these
880 :    
881 : bates 835 2005-03-03 Douglas Bates <bates@wisc.edu>
882 : bates 599
883 :     * src/lmer.c (lmer_fitted): Added.
884 :    
885 : bates 835 2005-03-02 Douglas Bates <bates@wisc.edu>
886 : bates 596
887 :     * R/dsTMatrix.R: Conversion from dsTMatrix to dsCMatrix
888 :    
889 : bates 835 2005-02-28 Douglas Bates <bates@wisc.edu>
890 : bates 582
891 :     * src/*.c,po/,inst/po: Internationalization and localization of
892 :     the package.
893 :    
894 :     * src/ldl.[ch]: Removed these as their contents are referenced in the
895 :     R_ldl.c file.
896 :    
897 :     * src/flame.[ch]: Removed these source files.
898 : maechler 658
899 : bates 582 * src/dtrMatrix.c (make_array_triangular): Move to Mutils
900 :    
901 :     * src/LU.[ch],src/init.c: absorb in factorizations
902 :    
903 :     * src/Mutils.h: prepare for internationalization
904 :    
905 :     * src/cblas.h: move the enum definitions to Mutils.h and remove
906 :     this file
907 :    
908 : maechler 578 2005-02-26 Martin Maechler <maechler@stat.math.ethz.ch>
909 :    
910 : maechler 579 * R/dgeMatrix.R: provide "dimnames" and "dimnames<-" methods
911 :    
912 :     * R/dtrMatrix.R: fix t() method
913 :    
914 : maechler 578 * R/dgeMatrix.R: define group methods "Arith", "Math", "Math2"
915 : maechler 658 * NAMESPACE: export them (and import generics from "methods")
916 : maechler 578 * tests/group-methods.R : and test them.
917 :    
918 :     * src/dtrMatrix.c (dtrMatrix_as_dgeMatrix): prevent seg.fault in
919 :     border case
920 :    
921 :     2005-02-24 Douglas Bates <bates@stat.wisc.edu>
922 :    
923 : maechler 658 * DESCRIPTION (Version): 0.95-2 released to CRAN
924 : maechler 578
925 :     * src/dgBCMatrix.c:
926 :     * src/lmer.c: many changes
927 :     * ...
928 :    
929 : maechler 512 2005-02-04 Martin Maechler <maechler@stat.math.ethz.ch>
930 :    
931 :     * R/Matrix.R: add more sophisticated show() method.
932 :    
933 : maechler 578 2005-02-02 Douglas Bates <bates@stat.wisc.edu>
934 :    
935 :     * */* : almost complete reorganization of classes.
936 :    
937 : bates 835 2005-01-26 Douglas Bates <bates@wisc.edu>
938 : bates 460
939 :     * R/AllGeneric.R: Added matrix exponential generic expm and a method
940 :     for the geMatrix class.
941 :    
942 : bates 835 2005-01-24 Douglas Bates <bates@wisc.edu>
943 : bates 460
944 :     * src/Makefile (clean): Remove *.a and *.so
945 :    
946 :     * man/cscBlocked-class.Rd: Remove reference to the lmer-class.
947 :    
948 : bates 835 2005-01-23 Douglas Bates <bates@wisc.edu>
949 : bates 460
950 : maechler 658 * src/lmer.c (Lind): Definition of Lind was backwards. This only
951 : bates 460 had an effect in cases with more than 2 grouping factors.
952 :    
953 : bates 835 2005-01-03 Douglas Bates <bates@wisc.edu>
954 : bates 415
955 :     * src/lmeRep.c (lmer_variances): change from lmeRep to lmer
956 :    
957 : bates 835 2004-12-23 Douglas Bates <bates@wisc.edu>
958 : bates 410
959 :     * src/init.c (R_init_Matrix): Reorder calls to R_registerRoutines
960 :     and R_useDynamicSymbols (suggested by B.D.Ripley).
961 :    
962 : bates 835 2004-12-14 Douglas Bates <bates@wisc.edu>
963 : bates 392
964 :     * R/sscMatrix.R: Add determinant methods
965 :    
966 :     * src/triplet.[ch],src/init.c (triplet_to_matrix): Add a coercion
967 :     for tripletMatrix to matrix.
968 :    
969 : bates 835 2004-12-13 Douglas Bates <bates@wisc.edu>
970 : bates 388
971 : bates 392 * R/AllClass.R (.onLoad): Eliminate the bbCrosstab class, which is
972 :     no longer used.
973 :    
974 : bates 388 * src/R_ldl.c: Created an R-specific version of the ldl.[ch] files
975 :     with dynamic allocation of scratch arrays.
976 :    
977 :     * src/ssclme.c (ssclme_copy_ctab): Fixed bug in creation of ZtZ
978 :     for multivariate random effects with multiple grouping factors.
979 :     Fixes part but not all of #15.
980 :    
981 : bates 835 2004-12-03 Douglas Bates <bates@wisc.edu>
982 : bates 375
983 :     * src/lmeRep.c (lmeRep_factor): order of operations for multiple
984 :     scalar grouping factors corrected.
985 :    
986 : bates 835 2004-11-29 Douglas Bates <bates@wisc.edu>
987 : bates 375
988 :     * src/bCrosstab.c: remove diag_update which is no longer used
989 :    
990 : bates 835 2004-11-16 Douglas Bates <bates@wisc.edu>
991 : bates 350
992 :     * src/Metis_utils.c: Move metis.h include to C sources so that the
993 :     .h file can be included.
994 :    
995 : bates 835 2004-11-12 Douglas Bates <bates@wisc.edu>
996 : bates 342
997 : bates 350 * src/LU.c,geMatrix.c,trMatrix.c, etc.:
998 : bates 342 Complete allocation of slots in NEW_OBJECT.
999 :    
1000 :     * src/Mutils.h: Moved list of symbols to an include file
1001 :    
1002 : bates 835 2004-11-11 Douglas Bates <bates@wisc.edu>
1003 : bates 342
1004 :     * src/geMutils.c (Matrix_init): remove unused function
1005 :    
1006 : bates 835 2004-11-10 Douglas Bates <bates@wisc.edu>
1007 : bates 342
1008 :     * src/cscMatrix.c (csc_to_imagemat): removed unused function
1009 :    
1010 : bates 835 2004-11-05 Douglas Bates <bates@wisc.edu>
1011 : bates 327
1012 :     * src/Makefile.win (SOURCES_C): Keep consistent with Makefile
1013 :    
1014 : bates 835 2004-10-27 Douglas Bates <bates@wisc.edu>
1015 : bates 303
1016 :     * R/pdmatrix.R: remove PACKAGE="Matrix" in .Call calls
1017 :    
1018 : bates 835 2004-10-04 Douglas Bates <bates@wisc.edu>
1019 : bates 296
1020 :     * src/init.c: Created R_init_Matrix and added registration of C
1021 :     routines.
1022 :    
1023 : bates 835 2004-10-02 Douglas Bates <bates@wisc.edu>
1024 : bates 283
1025 :     * R/tripletMatrix.R: Force a require(lattice) for the image methods.
1026 :    
1027 : bates 835 2004-06-15 Douglas Bates <bates@wisc.edu>
1028 : bates 229
1029 :     * man/trMatrix-class.Rd: Escape the % chars in .Rd files.
1030 :    
1031 : bates 111 2004-04-20 Douglas Bates <bates@stat.wisc.edu>
1032 :    
1033 :     * src/Makefile.win ($(SHLIB)): Modifications per Uwe Ligges.
1034 :    
1035 : bates 109 2004-04-19 Douglas Bates <bates@stat.wisc.edu>
1036 :    
1037 :     * src/ssclme.c (ssclme_update_mm): fix logic error in
1038 :     ssclme_update_mm
1039 :    
1040 : bates 105 2004-04-18 Douglas Bates <bates@stat.wisc.edu>
1041 :    
1042 :     * src/ssclme.c (ssclme_coef, ssclme_coefGets): Create consistency
1043 :     in the order of unconstrained and constrained parameters.
1044 :     (ssclme_gradient): Added the gradients (not yet correct for
1045 :     multidimensional, unconstrained case).
1046 :    
1047 : bates 78 2004-04-14 Douglas Bates <bates@stat.wisc.edu>
1048 :    
1049 :     * src/ssclme.c (ssclme_EMsteps): Fix logic in REML update
1050 :    
1051 :     * src/Makefile.win: Remove unneeded ranlib call
1052 :    
1053 : bates 71 2004-04-12 Douglas Bates <bates@stat.wisc.edu>
1054 :    
1055 :     * DESCRIPTION (Version): New release
1056 :    
1057 :     * src/Makefile.win: Update Makefile.win to umfpack removal.
1058 :    
1059 : bates 49 2004-04-05 Douglas Bates <bates@bates2_home>
1060 :    
1061 :     * src/triplet_to_col.c: Create triplet_to_col as a native
1062 : maechler 658 function, not the version from umfpack. There were problems with
1063 : bates 49 the configuration of UMFPACK for 64-bit processors and there was
1064 :     only one umfpack routine being used so I moved it here.
1065 :    
1066 : bates 45 2004-04-04 Douglas Bates <bates@bates2_home>
1067 :    
1068 :     * src/ssclme.c (ssclme_variances): New function.
1069 :    
1070 : bates 28 2004-03-28 Douglas Bates <bates@bates2_home>
1071 :    
1072 :     * src/ssclme.c (ssclme_fitted): Added function.
1073 :    
1074 : bates 22 2004-03-27 Douglas Bates <bates@bates2_home>
1075 :    
1076 :     * src/ssclme.c (ssclme_transfer_dimnames): Add new function to
1077 :     store the dimnames in the XtX and bVar slots
1078 :     (ssclme_update_mm): Change the dimensions of the bVar slot
1079 :     components and the returned value from ssclme_ranef.
1080 :    
1081 : bates 10 2004-03-18 Douglas Bates <bates@stat.wisc.edu>
1082 :    
1083 :     * R/{pdMat.R,pdIdent.R,pdLogChol.R,pdMatrixLog.R,pdNatural.R},
1084 :     src/{pdMat.c,pdIdent.c,pdLogChol.c,pdNatural.c},
1085 :     tests/{pdCompSymm.R,pdDiag.R,pdIdent.R,pdLogChol.R,pdNatural.R},
1086 :     man/{pdMat-class.Rd,pdmatrix-class.Rd,corrmatrix-class.Rd,
1087 :     pdDiag-class.Rd,pdIdent-class.Rd,pdNatural-class.Rd,
1088 :     pdLogChol-class.Rd,coefGets.Rd,pdCompSymm-class.Rd,
1089 :     pdfactor-class.Rd,pdFactor.Rd,pdMatrix.Rd,
1090 :     pdBlocked-class.Rd},AllClass.R,AllGeneric.R:
1091 :     Moved the pdMat classes from the lme4 package.
1092 :    
1093 :     2004-03-02 Douglas Bates <bates@stat.wisc.edu>
1094 :    
1095 :     * man/ssclme-class.Rd: Update definition and documentation of the
1096 :     ssclme class to include the DIsqrt slot.
1097 :    
1098 :     * src/ssclme.c (ssclme_deviance): Modify order of computation
1099 :     (much faster using dsyrk, a level 3 BLAS routine).
1100 :    
1101 :     * src/Makefile (SUBLIBS): Change definition (K. Hornik)
1102 :    
1103 :     2004-02-28 Douglas Bates <bates@stat.wisc.edu>
1104 :    
1105 :     * tests/ssclme.R: Modify the test to account for the permutation
1106 :     of the levels of the grouping factors.
1107 :    
1108 :     2004-02-23 Douglas Bates <bates@stat.wisc.edu>
1109 :    
1110 :     * R/ssclme.R,src/ssclme.c (ssclme): Move slots of sscCrosstab slot
1111 :     directly into the ssclme class definition.
1112 :    
1113 :     2004-02-22 Douglas Bates <bates@stat.wisc.edu>
1114 :    
1115 :     * DESCRIPTION (Date): New release
1116 :    
1117 :     * man/ssclme-class.Rd: new file.
1118 :    
1119 :     * src/ssclme.c (ssclme_loglik): major revisions in design. It
1120 :     works and it's fast!
1121 :    
1122 :     2004-02-17 Douglas Bates <bates@stat.wisc.edu>
1123 :    
1124 :     * src/taucs/Makefile.win (lib): Change "ar" to "$(AR)" (B.Ripley)
1125 :    
1126 :     2004-02-16 Douglas Bates <bates@stat.wisc.edu>
1127 :    
1128 :     * DESCRIPTION (Date): New release
1129 :    
1130 :     * NAMESPACE: Don't export ssclme.
1131 :    
1132 :     * data/ScotsSec.rda, man/ScotsSec.Rd: Add Scottish secondary
1133 :     school data.
1134 :    
1135 :     2004-02-11 Douglas Bates <bates@stat.wisc.edu>
1136 :    
1137 :     * src/sscCrosstab.c (sscCrosstab): Added a row to the incidence to
1138 :     keep track of the fixed-effects and the response. Counts also
1139 :     gets an extra element, which is always one.
1140 :    
1141 :     * src/ldl.c: Include these routines from Tim Davis' LDL package.
1142 :    
1143 :     2004-02-10 Douglas Bates <bates@stat.wisc.edu>
1144 :    
1145 :     * src/cscMatrix.c (csc_transpose): new function
1146 :    
1147 :     * src/Mutils.c (csc_sort_columns): perm/iperm confusion corrected
1148 :     (csc_components_transpose): new function
1149 :    
1150 :     2004-02-06 Douglas Bates <bates@stat.wisc.edu>
1151 :    
1152 :     * src/triplet.c (triplet_validate): Fix Dim slot on generated
1153 :     triplets
1154 :    
1155 :     2004-01-30 Douglas Bates <bates@stat.wisc.edu>
1156 :    
1157 :     * R/sscCrosstab.R (sscCrosstab): Added sscCrosstab generator function.
1158 :    
1159 :     * src/LU.h (MATRIX_LU_H): Add #ifndef #define ... #endif to this
1160 :     and all other .h files in src.
1161 :    
1162 :     * src/Makefile.win: This and other Makefile.win files contributed
1163 :     by Brian Ripley.
1164 :    
1165 :     2004-01-27 Douglas Bates <bates@stat.wisc.edu>
1166 :    
1167 :     * R/syMatrix.R: Added methods for "%*%".
1168 :    
1169 :     * R/Hilbert.R (Hilbert): Changed Hilbert function to return a
1170 :     poMatrix object.
1171 :    
1172 :     2004-01-26 Douglas Bates <bates@stat.wisc.edu>
1173 :    
1174 :     * man/sscChol-class.Rd,man/mm.Rd,man/y.Rd: Added man pages.
1175 :    
1176 :     2004-01-25 Douglas Bates <bates@bates2_home>
1177 :    
1178 :     * inst/doc/Introduction.Rnw,Comparisons.Rnw: Added vignettes.
1179 :    
1180 :     * R/csc.R: Convert all cscMatrix classes to use Dim slot instead
1181 :     of nrow.
1182 :    
1183 :     2003-12-31 Douglas Bates <bates@stat.wisc.edu>
1184 :    
1185 :     * src/taucs/taucs.h: Moved taucs.h, amd.h, and umfpack.h into
1186 :     subdirectories.
1187 :    
1188 :     2003-12-08 Douglas Bates <bates@stat.wisc.edu>
1189 :    
1190 :     * src/taucs.h: Accidently referred to global header files
1191 :     instead of local files.
1192 :    
1193 :     2003-12-04 Douglas Bates <bates@stat.wisc.edu>
1194 :    
1195 :     * R/AllClass.R: Lots of changes. Removed all the lapack++ code
1196 :     and methods and replaced all classes with S4 classes.
1197 :    
1198 :     2003-04-19 Douglas Bates <bates@stat.wisc.edu>
1199 :    
1200 :     * R/det.R,man/det.Rd: Change name of det generic to determinant
1201 :    
1202 :     * src/R_LapackPP.cc: Change method of calculating determinants
1203 :    
1204 :     2003-02-03 Douglas Bates <bates@stat.wisc.edu>
1205 :    
1206 :     * DESCRIPTION (Version): removed empty data directory as requested
1207 :     by CRAN maintainers. Changed version number and date.
1208 :    
1209 :     2002-10-23 Douglas Bates <bates@stat.wisc.edu>
1210 :    
1211 :     * src/laindex.h: Applied patches from Brian Ripley for compilation
1212 :     under Windows.
1213 :    
1214 :     * Added configure.win and src/Makevars.win as requested by Brian
1215 :     Ripley.
1216 :    
1217 :     2002-05-03 Douglas Bates <bates@stat.wisc.edu>
1218 :    
1219 :     * src/lamatrix.h: Removing pre-1.2.0 compatibility code per Kurt
1220 :     Hornik.
1221 :    
1222 :     2002-04-24 Douglas Bates <bates@stat.wisc.edu>
1223 :    
1224 :     * configure.ac: Replaced configure.in with configure.ac
1225 :     contributed by Kurt Hornik.
1226 :    
1227 :     * aclocal.m4 (ac_clean_files): Replaced this with Kurt Hornik's
1228 :     version for R-1.5.0
1229 :    
1230 : maechler 512
1231 : bates 10 2001-12-10 Douglas Bates <bates@stat.wisc.edu>
1232 :    
1233 :     * man/eigen.Rd: Removed the .Alias in the example

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