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

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