SCM

SCM Repository

[matrix] Annotation of /pkg/ChangeLog
ViewVC logotype

Annotation of /pkg/ChangeLog

Parent Directory Parent Directory | Revision Log Revision Log


Revision 1368 - (view) (download)

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

root@r-forge.r-project.org
ViewVC Help
Powered by ViewVC 1.0.0  
Thanks to:
Vienna University of Economics and Business Powered By FusionForge