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Annotation of /pkg/ChangeLog

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

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