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1 : bates 1414 2006-08-22 Douglas Bates <bates@R-project.org>
2 :    
3 :     * src/Mutils.c (dup_mMatrix_as_dgeMatrix): updated for general
4 :     types of classed Matrices, matrices or numeric or logical vectors.
5 : bates 1423 * src/init.c: register dup_mMatrix_as_dgeMatrix for coercions.
6 :     * src/chm_common.c,Mutils.h (as_cholmod_factor): Move check_class
7 :     to Mutils.h (as an inline) and change name to Matrix_check_class;
8 :     fixes in as_cholmod_factor and chm_factor_to_SEXP.
9 :     * src/dsCMatrix.[ch]: Use CHOLMOD for dsCMatrix_chol and
10 :     dsCMatrix_matrix_solve. Comment out vestigial functions.
11 :     * src/Csparse.c: use diag_P and uplo_P macros.
12 : bates 1420
13 : bates 1405 2006-08-21 Douglas Bates <bates@R-project.org>
14 :    
15 :     * src/lmer.c (internal_mer_RZXinv): Fix memory leak caught by
16 :     valgrind.
17 : bates 1411 * tests/matprod.R: Add tests to verify that 'solve' and '%*%' are
18 :     inverses.
19 :     * src/sparseQR.c (sparseQR_validate): add new validation test, fix
20 :     -Wall warnings.
21 :     * src/dppMatrix.c,dtrMatrix.c,dgCMatrix.c,dgeMatrix.c,dspMatrix.c:
22 :     Use dup_mMatrix_as_dgeMatrix.
23 :    
24 : bates 1403 2006-08-20 Douglas Bates <bates@R-project.org>
25 :    
26 :     * src/sparseQR.c: Fix thinko in sparseQR_resid_fitted.
27 :     * tests/sparseQR.R: Added
28 :     * man/sparseQR-class.Rd: Document methods for qr.* generics
29 :     * R/sparseQR.R: Return correct # of coefs; fix cut-and-paste errors
30 :    
31 : bates 1398 2006-08-19 Douglas Bates <bates@R-project.org>
32 :    
33 :     * NAMESPACE, R/sparseQR.R, src/init.c,sparseQR.[ch],SOURCES_C.mkf:
34 :     Added methods for sparseQR for qr.qy, qr.qty, qr.coef, qr.resid
35 :     and qr.fitted.
36 :     * src/Mutils.[ch]: Added dup_mMatrix_as_dgeMatrix utility
37 :     * src/dgCMatrix.c: Check for ordering before storing q in dgCMatrix_QR
38 :    
39 : maechler 1389 2006-08-18 Martin Maechler <maechler@stat.math.ethz.ch>
40 :    
41 :     * R/AllGeneric.R: add "qr" and "chol" generics; via 'trick' since
42 :     the base version has no "..." argument.
43 :    
44 :     * R/sparseMatrix.R (prSpMatrix): fix the triangular unit diagonal case.
45 :    
46 :     * R/Matrix.R: define and
47 :     * NAMESPACE: export as.numeric() and as.logical() methods.
48 :     Let's hope these do not badly slow down something...
49 :     Finally export the zapsmall() method.
50 :    
51 : bates 1388 2006-08-17 Douglas Bates <bates@R-project.org>
52 :    
53 :     * src/dgCMatrix.[ch] (dgCMatrix_matrix_solve), src/init.c,
54 :     R/dgCMatrix.R: solve methods for dgCMatrix and dense RHS.
55 :     * src/dtCMatrix.c :Remove code that is no longer used
56 :     * R/dtCMatrix.R: Use C code for diagU2N in CsparseMatrix classes
57 :    
58 : bates 1370 2006-08-14 Douglas Bates <bates@R-project.org>
59 :    
60 : bates 1373 * src/Csparse.[ch],init.c (Csparse_to_logical): Added utilities
61 :     Csparse_to_logical and Csparse_symmetric_to_general.
62 :     * R/dgCMatrix.R,dsCMatrix.R,Csparse.R : Consolidate general
63 : maechler 1389 coercion methods between CsparseMatrix and TsparseMatrix.
64 : bates 1373
65 :     2006-08-14 Douglas Bates <bates@R-project.org>
66 :    
67 : bates 1370 * R/dtCMatrix.R,dgCMatrix.R,Csparse.R src/init.c,dgCMatrix.[ch],
68 :     Csparse.[ch],chm_common.c,dense.c : Use CHOLMOD code and methods
69 :     for CsparseMatrix, TsparseMatrix, denseMatrix or matrix when
70 :     possible.
71 :    
72 : bates 1368 2006-08-12 Douglas Bates <bates@R-project.org>
73 :    
74 :     * src/chm_common.[ch],Csparse.[ch],Tsparse.[ch],CHMfactor.c,dtTMatrix.c,
75 :     dgTMatrix.c,dgCMatrix.c,dsCMatrix.c,dtTMatrix.c, R/dsTMatrix.R,
76 :     Tsparse.R,Csparse.R,dgTMatrix.R,dsCMatrix.R,lsCMatrix.R:
77 :     generalize conversions between TsparseMatrix, CsparseMatrix,
78 :     denseMatrix and matrix. Preserve triangularity property and
79 :     propagate Dimnames in the easy cases.
80 :    
81 : bates 1365 2006-08-10 Douglas Bates <bates@R-project.org>
82 :    
83 :     * src/lmer.c: adjust checks in glmer_init for S4SXP
84 :     * tests/validObj.R: check of all(eq) should be all(eq@x) - worked
85 :     before S4SXP but for the wrong reasons.
86 :    
87 : bates 1354 2006-08-08 Douglas Bates <bates@R-project.org>
88 :    
89 : bates 1360 * src/Csparse.c (Csparse_crossprod): tcrossprod result has stype = -1.
90 :     Later modified to return the upper triangle only.
91 :     * R/dgTMatrix.R: Remove vestigial crossprod and tcrossprod methods.
92 : maechler 1389
93 : bates 1352 2006-08-07 Douglas Bates <bates@R-project.org>
94 :    
95 :     * src/Csparse.c (Csparse_crossprod): Set stype on result to avoid
96 :     R-level conversion to a sparse symmetric class.
97 :     * R/Tsparse.R,R/Csparse.R (crossprod and tcrossprod methods):
98 :     Remove conversion to sparse symmetric classes (now done in C code).
99 :    
100 : maechler 1349 2006-08-07 Martin Maechler <maechler@stat.math.ethz.ch>
101 :    
102 : maechler 1351 * R/dgCMatrix.R: disable old crossprod and tcrossprod methods
103 :     * man/band.Rd: adapt the \dontshow{} unit test.
104 :    
105 :     2006-08-07 Martin Maechler <maechler@stat.math.ethz.ch>
106 :    
107 : maechler 1349 * DESCRIPTION (Version): 0.995-14 for CRAN
108 :    
109 :     * tests/other-pkgs.R: oops: library(Matrix) outside *if* !
110 :    
111 :     * R/sparseMatrix.R (Tsp2grNEL): fixed Tsparse -> graph coercion
112 :     * tests/other-pkgs.R: more checks, sparseMatrix -> graph
113 :    
114 :     * R/Auxiliaries.R (as_Tsparse, as_Rsparse): new
115 :     * R/Tsparse.R (tril, triu, band): methods
116 : bates 1352 * R/dgRMatrix.R (tril, ...): ditto
117 :     * man/band.Rd: ditto
118 : maechler 1349
119 :     2006-08-04 Martin Maechler <maechler@stat.math.ethz.ch>
120 :    
121 :     * R/Matrix.R (head, tail): directly use utils:::head.matrix
122 :     to be up-to-date automatically.
123 :    
124 : maechler 1346 2006-08-03 Martin Maechler <maechler@stat.math.ethz.ch>
125 :    
126 :     * DESCRIPTION (Version): 0.995-13 to be released to CRAN
127 :    
128 :     * DESCRIPTION (Lazydata): no, instead of 'yes' because it fails for:
129 :     * data/CAex.R, inst/external/CAex_slots.rda: replacing data/CAex.rda
130 :     * data/KNex.R, inst/external/KNex_slots.rda: replacing data/KNex.rda
131 :     such that the S4 objects are always created by the current version
132 :     of R and 'Matrix' class definitions.
133 :    
134 : bates 1342 2006-08-01 Douglas Bates <bates@R-project.org>
135 :    
136 :     * R/lmer.R (LMEoptimize method), tests/lmer.R,
137 : maechler 1346 inst/external/test3comp.rda: Added warnings for convergence on
138 : bates 1342 boundary and test cases.
139 :    
140 :     * src/lmer.c (mer_postVar): Modified to return the variances that
141 :     are marginal to the fixed effects, not conditional on them (which
142 :     is what the bVar slot contents represent).
143 :    
144 : bates 1338 2006-07-31 Douglas Bates <bates@R-project.org>
145 :    
146 :     * NAMESPACE, src/lmer.c, R/lmer.R (hatTrace): Add the hatTrace
147 :     function which calls the C function mer_hat_trace2.
148 : maechler 1346
149 : bates 1342 * man/ranef.Rd: Include description of "postVar" argument and
150 :     producing a caterpillar plot.
151 : bates 1338
152 : maechler 1335 2006-07-31 Martin Maechler <maechler@stat.math.ethz.ch>
153 :    
154 :     * NAMESPACE: change "correlation" to "corMatrix"
155 :     * R/AllClass.R: to avoid clash with S3 class in 'nlme'.
156 : bates 1352 * R/dpoMatrix.R: ditto
157 :     * R/lmer.R: ditto
158 : maechler 1335
159 : bates 1338 2006-07-28 Douglas Bates <bates@R-project.org>
160 :    
161 :     * src/lmer.c (internal_mer_RZXinv): Split the calculation of the
162 :     RZXinv slot's contents into a separate internal function that can
163 :     be used in mer_hat_trace.
164 :    
165 : maechler 1331 2006-07-22 Martin Maechler <maechler@stat.math.ethz.ch>
166 :    
167 :     * R/Matrix.R: Coercions "Matrix" -> (sparse|dense)Matrix
168 :     via new smart
169 :     * R/Auxiliaries.R (as_Csparse, as_dense, .M.shapse): new
170 :     utility functions.
171 :    
172 :    
173 : maechler 1330 2006-07-21 Martin Maechler <maechler@stat.math.ethz.ch>
174 :    
175 : maechler 1331 * R/Csparse.R (tril, triu, band): do return *triangular* classed
176 :     matrices when appropriate; band() even symmetric ones.
177 :     (replCmat): extend to potentially all "CsparseMatrix"
178 :     * R/Tsparse.R (replTmat): extend to all "TsparseMatrix"; hence
179 :     allow subassignment for special sparse matrices.
180 :    
181 :     * R/Auxiliaries.R (as_geClass): factor out the .M.kind() functionality
182 :    
183 : maechler 1330 * src/lmer.c (mer_MCMCsamp, glmer_MCMCsamp): new 'verbose'
184 :     argument; in glmer_*(): print only if(verbose).
185 :    
186 :     speed-optimize a few places by moving REAL(.) out of loops.
187 :    
188 :     * src/lmer.h, src/init.h, R/lmer.R: related to above.
189 :    
190 : maechler 1329 2006-07-20 Martin Maechler <maechler@stat.math.ethz.ch>
191 :    
192 :     * R/Matrix.R("["): disable ("Matrix", i = "logical", j = "missing"),
193 :     since that wrongly triggers also for M[ logi , ]
194 :    
195 :     * R/denseMatrix.R: "[" methods now also work e.g. when indexing
196 :     a symmetric matrix that results in a non-symmetric one.
197 :     * R/Auxiliaries.R (as_geClass): new function used in "[" above.
198 :    
199 :     * R/dMatrix.R: make round(M) work as round(M, 0)
200 :    
201 :     * R/dgTMatrix.R (image): coordinate system and axis now use
202 :     1-based indices, not 0-based ones.
203 :    
204 :     * R/Tsparse.R (.ind.prep for "["): get rid of max(<empty>) warning.
205 :     * tests/indexing.R: test it.
206 :    
207 :     * NAMESPACE: export isSymmetric(); has been a generic in "base" for a while;
208 :     * man/isSymmetric-methods.Rd: and document it.
209 :    
210 :     * R/SparseM-conv.R: added coercion methods for some 'SparseM' matrices.
211 :     * man/SparseM-conv.Rd: docu them
212 :    
213 :     * tests/other-pkgs.R: renamed from tests/graph.R and add example
214 :     for 'SparseM' conversions
215 :    
216 :     2006-07-17 Douglas Bates <Douglas.Bates@R-project.org>
217 :    
218 :     * R/Matrix.R (head): added head() and tail() methods.
219 :    
220 :     2006-07-17 Martin Maechler <maechler@stat.math.ethz.ch>
221 :    
222 :     * DESCRIPTION (Version): 0.995-12 released to CRAN
223 :    
224 : maechler 1319 2006-07-15 Martin Maechler <maechler@stat.math.ethz.ch>
225 :    
226 :     * tests/simple.R: add check for correct dsT -> dgT coercion;
227 :     add check for correct printing of symmetric sparse matrices.
228 :    
229 :     * R/Auxiliaries.R (non0ind): return *all* non-0 entry indices also
230 :     for sparse symmetric matrices.
231 :    
232 :     * src/dsTMatrix.c (dsTMatrix_as_dgTMatrix): do not copy the
233 :     diagonal twice.
234 :    
235 : bates 1316 2006-07-11 Douglas Bates <Douglas.Bates@R-project.org>
236 :    
237 :     * src/dsTMatrix.c (dsTMatrix_as_dgTMatrix): Fix a case of INTEGER
238 : maechler 1319 being applied to the x slot (detected by Brian Ripley).
239 : bates 1316
240 : maechler 1315 2006-07-10 Martin Maechler <maechler@stat.math.ethz.ch>
241 :    
242 :     * src/dgCMatrix.c (dgCMatrix_validate): 'p' slot must have correct length.
243 :    
244 :     * R/Auxiliaries.R (isTriC): fix buglet (we were 1-based!)
245 :    
246 :     2006-07-08 Martin Maechler <maechler@stat.math.ethz.ch>
247 :    
248 :     * src/lgCMatrix.c (lgCMatrix_diag): new function
249 :     * R/lgCMatrix.R (diag): for new method
250 :    
251 :     * R/AllClass.R (TsparseMatrix): do use Tsparse_validate
252 :     ==> construction of illegal "*gTMatrix" via new() should
253 :     now be much less easy:
254 :     * tests/Class+Meth.R: assertError() for some illegal "dgT*"
255 :    
256 :     * R/Matrix.R (Matrix): Matrix(0, nrow,ncol) now "goes sparse"
257 :     directly.
258 :     * man/Matrix.Rd: documents it.
259 :    
260 : bates 1311 2006-07-06 Douglas Bates <bates@R-project.org>
261 :    
262 :     * src/pedigree.c (pedigree_inbreeding): Correction in
263 :     initialization. This function is not currently being used and is
264 :     not fully tested.
265 :    
266 : bates 1312 * NAMESPACE, R/{AllClass.R,lmer.R}, src/{init.c,lmer.c}:
267 :     Introduced the glmer class. Added code for mcmcmsamp on glmer
268 :     objects. Modified validity check on pedigree objects to account
269 :     for nonparallel patterns of missingness of parents.
270 : bates 1311
271 : bates 1313 * man/{lmer-class.Rd,mcmcsamp.Rd}: Update documentation for glmer
272 :     class.
273 : maechler 1315
274 :     2006-07-01 Martin Maechler <maechler@stat.math.ethz.ch>
275 :    
276 :     * R/pMatrix.R: coercion pMatrix -> Tsparse
277 :    
278 : bates 1300 2006-06-12 Douglas Bates <bates@R-project.org>
279 :    
280 : maechler 1319 * DESCRIPTION (Version): 0.995-11 released to CRAN
281 :    
282 : bates 1300 * R/lmer.R (mcmcsamp method): Corrected arrangments of names on
283 :     the output from mcmcsamp.
284 :    
285 : bates 1298 2006-06-10 Douglas Bates <bates@R-project.org>
286 :    
287 : bates 1300 * R/lmer.R (simulestimate): added C code for calculating the trace
288 :     of the hat matrix.
289 : bates 1298
290 : maechler 1295 2006-06-09 Martin Maechler <maechler@stat.math.ethz.ch>
291 :    
292 :     * R/diagMatrix.R (setAs): define coercion methods to sparse matrix
293 :     classes.
294 : maechler 1315 * R/sparseMatrix.R etc: multiplication of diagonal and sparse
295 : maechler 1295
296 : maechler 1290 2006-06-08 Martin Maechler <maechler@stat.math.ethz.ch>
297 :    
298 :     * R/dgTMatrix.R (colSums): etc. All four of
299 :     colSums(), rowSums(), colMeans(), rowMeans() now should work for
300 :     all "Matrices".
301 :    
302 : bates 1288 2006-06-01 Douglas Bates <bates@stat.wisc.edu>
303 :    
304 :     * R/lmer.R (panel.ci): Add a reference line at zero and a
305 :     background grid to the qqmath plot of ranef.lmer.
306 :    
307 : bates 1287 2006-05-30 Douglas Bates <bates@stat.wisc.edu>
308 : bates 1284
309 : bates 1287 * R/lmer.R (expandSlash): Functions (non-exported) to allow nested
310 :     grouping factors to be specified in the formula as (1|foo/bar).
311 :    
312 :     2006-05-27 Douglas Bates <bates@stat.wisc.edu>
313 :    
314 : bates 1284 * R/lmer.R (findbars and others): Change check of is.numeric to
315 :     !is.language to resolve the bug reported by Jacob Wegelin.
316 :    
317 :     * src/pedigree.c (pedigree_inbreeding): Initial implementation of
318 :     code to evaluate inbreeding coefficients without calculating T,
319 :     based on code in Sargolzaei and Iwaisaki's paper.
320 :    
321 : bates 1283 2006-05-27 Douglas Bates <bates@stat.wisc.edu>
322 :    
323 :     * R/{lmer.R,AllGeneric.R}, src/{init.c,lmer.[ch]}: Added local
324 :     generic and mer methods for isNested and denomDF. This denomDF was
325 :     an attempt to emulate that in lme but I don't think that makes
326 :     sense. Use the trace of the hat matrix instead.
327 :    
328 : maechler 1271 2006-05-17 Martin Maechler <maechler@stat.math.ethz.ch>
329 :    
330 :     * R/sparseMatrix.R: Matrix <-> graph methods: can no longer use
331 :     the C code depending on a slot structure that's no longer valid.
332 : bates 1352 * src/dgTMatrix.c: ditto (also: src/init.c src/dgTMatrix.h)
333 : maechler 1271
334 :    
335 : bates 1268 2006-05-17 Douglas Bates <bates@stat.wisc.edu>
336 :    
337 :     * R/{AllGeneric.R,Csparse.R},man/band.Rd,NAMESPACE: changed name
338 :     of lowerTriMatrix generic and methods to tril (also upper to triu)
339 :     and added a general band extractor.
340 :    
341 : bates 1267 2006-05-16 Douglas Bates <bates@stat.wisc.edu>
342 :    
343 :     * R/pedigree.R (pedigree): Replace sire and dam values outside the
344 :     allowable range with NAs. Added a corresponding check in the
345 :     validity check for the pedigree class.
346 :    
347 :     * R/[CT]sparse.R ([t]crossprod): The result of single-argument
348 :     crossprod methods now inherits from symmetricMatrix.
349 :    
350 : bates 1265 2006-05-15 Douglas Bates <bates@stat.wisc.edu>
351 :    
352 :     * R/AllGeneric.R (lowerTriMatrix): Added (but did not export)
353 :     generics lowerTriMatrix and upperTriMatrix along with methods for
354 :     the Csparse virtual class. Also added a C function Csparse_band
355 :     that implements these methods by calling cholmod_band.
356 :    
357 : maechler 1264 2006-05-15 Martin Maechler <maechler@stat.math.ethz.ch>
358 :    
359 :     * R/Tsparse.R ("["): column or row subsetting; @Dimnames[k] got
360 :     erased when it was NULL. This led to invalid subselections!
361 :    
362 : bates 1259 2006-04-25 Douglas Bates <bates@stat.wisc.edu>
363 :    
364 :     * R/dtCMatrix.R: avoid coercion of dtCMatrix object to dgCMatrix
365 :     in method for "t" so as not to lose the unit diagonal property.
366 :    
367 : bates 1257 2006-04-19 Douglas Bates <bates@stat.wisc.edu>
368 :    
369 :     * R/lmer.R, R/AllGeneric.R, NAMESPACE: Remove the postVar generic
370 :     and methods. This is now an option to the ranef method for the
371 :     mer class.
372 :    
373 :     * src/cs_utils.c: Ensure that the nz component is -1 for a
374 :     compressed column-oriented matrix. Minor formatting cleanup.
375 :    
376 :     * man/lmer-class.Rd: Document the qqmath method for ranef.lmer
377 :     objects.
378 :    
379 : maechler 1253 2006-04-19 Martin Maechler <maechler@stat.math.ethz.ch>
380 :    
381 :     * R/Auxiliaries.R (diagU2N): new for the solve() methods in
382 :     * R/dtCMatrix.R: where dgC -> dgT coercion now preserves diag = "U".
383 :    
384 : bates 1251 2006-04-15 Douglas Bates <bates@stat.wisc.edu>
385 :    
386 :     * src/cs.[ch],src/cs_utils.[ch] : Added Tim Davis' CSparse library
387 :     in cs.[ch] and utilities to interface to that code in cs_utils.[ch].
388 :    
389 :     * R/dtCMatrix.R, src/dtCMatrix.[ch] : CSparse-based solve methods
390 :     for the dtCMatrix class.
391 : maechler 1253
392 : bates 1247 2006-04-12 Douglas Bates <bates@stat.wisc.edu>
393 :    
394 :     * R/pedigree.R, R/AllClass.R, NAMESPACE: added a pedigree class
395 :     and methods for it.
396 :    
397 : maechler 1245 2006-04-12 Martin Maechler <maechler@stat.math.ethz.ch>
398 :    
399 :     * R/dgCMatrix.R: add storage.mode(.) <- "double" for "matrix"
400 :     arguments, such that M %*% 1:6 now works
401 :     * Tests/matprod.R: test the above
402 :    
403 : bates 1244 2006-04-03 Douglas Bates <bates@stat.wisc.edu>
404 : bates 1243
405 :     * R/lmer.R (qqmath,ranef.lmer-method): added a qqmath method for
406 :     the ranef.lmer class.
407 :    
408 :     * R/AllClass.R, NAMESPACE, R/lmer.R: Added a postVar generic and
409 :     methods to extract the posterior variances from the bVar slot.
410 :    
411 : maechler 1238 2006-03-30 Martin Maechler <maechler@stat.math.ethz.ch>
412 :    
413 :     * R/dtCMatrix.R: allow coercion from dgC* to triangular (dtC*)
414 :     * R/dsCMatrix.R: and symmetric (dsC*) 'Csparse' matrices.
415 :    
416 :     * R/Tsparse.R: Tsparse* -> Csparse* coercion now works and is tested in
417 :     * tests/simple: (extended)
418 :    
419 :     * R/sparseMatrix.R (isTriangular): now using much improved
420 :     * R/Auxiliaries.R (isTriC): new triangularity check for *CMatrix
421 :    
422 : bates 1236 2006-03-23 Douglas Bates <bates@stat.wisc.edu>
423 :    
424 :     * src/dsyMatrix.c (dsyMatrix_as_dspMatrix): Propagate DimNames
425 :     (problem report from Franklin Parlamis). This should be done
426 : maechler 1238 generally.
427 : bates 1236
428 : bates 1234 2006-03-21 Douglas Bates <bates@stat.wisc.edu>
429 :    
430 :     * R/AllClass.R,lmer.R: Change the name of the lmer.ranef class to
431 :     ranef.lmer (like summary.lmer). Add the coef.lmer class and
432 :     update the plot methods.
433 :    
434 : bates 1232 2006-03-20 Douglas Bates <bates@stat.wisc.edu>
435 :    
436 :     * R/lmer.R (resid and ranef methods): Added methods for the
437 :     "residuals" and "resid" generic but only for linear mixed model
438 :     fits. Changed the ranef method to return a list of data frames so
439 :     that the plot methods now work.
440 :    
441 : bates 1230 2006-03-16 Douglas Bates <bates@bates2>
442 :    
443 :     * src/dpoMatrix.c (dpoMatrix_chol): Require n > 0 in call to
444 :     dpotrf - otherwise the BLAS on Mac OS X complains and quits.
445 :    
446 :     * DESCRIPTION (Date): New release
447 :    
448 : maechler 1228 2006-03-15 Martin Maechler <maechler@stat.math.ethz.ch>
449 :    
450 :     * DESCRIPTION (Version): 0.995-6 -- to be released to CRAN
451 :    
452 :     * data/KNex.rda: replacing 'mm' and 'y' by KNex <- list(mm=mm, y=y)
453 :     * man/KNex.Rd: and other help files
454 :     * tests/*.R: several ones needed adaption
455 : bates 1352 * inst/doc/Comparisons.Rnw: ditto
456 : maechler 1228
457 : maechler 1226 2006-03-11 Martin Maechler <maechler@stat.math.ethz.ch>
458 :    
459 :     * R/dgCMatrix.R (replCmat): "[<-" methods for dgCMatrix
460 :    
461 :     * tests/indexing.R: tests for new [<- methods for sparse matrices.
462 :    
463 :     2006-03-10 Martin Maechler <maechler@stat.math.ethz.ch>
464 :    
465 :     * R/dgTMatrix.R (replTmat): "[<-" methods for dgTMatrix
466 :    
467 :     * R/Tsparse.R (.ind.prep): fix out-of-range indexing
468 :    
469 :     2006-03-08 Martin Maechler <maechler@stat.math.ethz.ch>
470 :    
471 :     * R/dMatrix.R: enable things like M [ M < 10 ]
472 :     * R/dgeMatrix.R: implement it
473 :    
474 : maechler 1222 2006-03-06 Martin Maechler <maechler@stat.math.ethz.ch>
475 :    
476 :     * R/AllClass.R: define "summary.mer" and "*.lmer"
477 :     * R/lmer.R (summary): summary(<mer>) computes & returns the above;
478 :     * R/lmer.R (show): now works with summary()
479 :    
480 :     2006-03-04 Martin Maechler <maechler@stat.math.ethz.ch>
481 :    
482 :     * R/dgCMatrix.R: finally direct "Arith" dgC o dgC
483 :     * R/Auxiliaries.R (WhichintersectInd): and other utilities to
484 :     support the above
485 :    
486 : bates 1213 2006-02-07 Douglas Bates <bates@stat.wisc.edu>
487 :    
488 :     * R/lmer.R (lmer): fix initial values of offset and weights for glm.fit.
489 :     Use glmFit$prior.weights for weights in a glmm.
490 :     Allow an option usePQL = FALSE to skip the PQL steps for the
491 :     Laplace method (and, in time, the AGQ method).
492 :    
493 :     * src/lmer.c (mer_factor): Move downdating and factoring of XtX
494 :     into a separate function internal_mer_Xfactor to be able to call
495 :     it from internal_bhat.
496 :    
497 : maechler 1200 2006-01-23 Martin Maechler <maechler@stat.math.ethz.ch>
498 :    
499 :     * tests/Class+Meth.R (tstMatrixClass): function for much better
500 :     testing; now again of all actual classes.
501 :    
502 :     * src/Mutils.c (MAKE_TRIANGULAR_BODY, MAKE_SYMMETRIC_BODY):
503 :     use macros and define make_d_matrix_* and make_i_matrix_*
504 :     where _i_ is for the ldense routines:
505 :    
506 :     * src/ldense.c (ltrMatrix_as_lgeMatrix): provide functions
507 :     * src/ldense.c (lsyMatrix_as_lgeMatrix):
508 :    
509 :     * R/ldenseMatrix.R: use the above in setAs(*,"lgeMatrix")
510 :    
511 :    
512 : maechler 1174 2006-01-16 Martin Maechler <maechler@stat.math.ethz.ch>
513 :    
514 :     * R/Matrix.R (Matrix): has become much "smarter" now auto-producing
515 :     many different kinds of matrices.
516 :     * R/*.R: quite a few new methods were needed for R CMD check with
517 :     new Matrix(). Very good for users playing around.
518 :    
519 :    
520 : maechler 1165 2006-01-15 Martin Maechler <maechler@stat.math.ethz.ch>
521 :    
522 :     * src/dgeMatrix.c (dMatrix_validate): new
523 :     * src/Mutils.c (dense_nonpacked_validate): new
524 :    
525 :     * src/dtrMatrix.c (dtrMatrix_validate): improved/fixed
526 :    
527 :    
528 :     2006-01-14 Douglas Bates <bates@stat.wisc.edu>
529 :    
530 :     * R/AllClass.R (compMatrix), (generalMatrix): new virtual classes
531 :    
532 : bates 1123 2006-01-07 Douglas Bates <bates@stat.wisc.edu>
533 : bates 1119
534 : maechler 1127 * DESCRIPTION (Version): 0.99-6 released to CRAN
535 :    
536 : bates 1119 * src/dgBCMatrix.c (cscb_trcbsm): Fix due to Peter Dalgaard for
537 :     segfault in cases with multiple non-nested grouping factors.
538 :    
539 : maechler 1109 2006-01-03 Martin Maechler <maechler@stat.math.ethz.ch>
540 :    
541 :     * DESCRIPTION (Version): 0.99-4 to be released to CRAN
542 :     (Depends): also on 'utils'
543 :    
544 :     * R/AllClass.R (diagonalMatrix): new class with "ddi*" and "ldi*"
545 :     * R/diagMatrix.R (Diagonal): constructor and methods for
546 :     diagonal matrices
547 :    
548 :     * R/ltTMatrix.R: new "minimal methods"
549 :    
550 : maechler 1091 2005-12-12 Martin Maechler <maechler@stat.math.ethz.ch>
551 :    
552 :     * R/AllGeneric.R (tcrossprod): 2-argument version; here, and for
553 :     all methods (and help files).
554 :    
555 : maechler 1084 2005-12-09 Martin Maechler <maechler@stat.math.ethz.ch>
556 :    
557 :     * R/Auxiliaries.R (dimNamesCheck): fixed thinko -> bug
558 :     for case (dimn. op no_dimn.)
559 :    
560 :     2005-11-14 Douglas Bates <bates@stat.wisc.edu>
561 :    
562 : maechler 1174 * DESCRIPTION (Version): 0.99-2 released to CRAN
563 : maechler 1084
564 : bates 988 2005-10-21 Douglas Bates <bates@stat.wisc.edu>
565 :    
566 :     * R/lmer.R (simulate method): Fixed a drop=FALSE problem reported
567 :     by Julian Faraway.
568 :    
569 : maechler 976 2005-10-06 Martin Maechler <maechler@stat.math.ethz.ch>
570 :    
571 :     * R/Auxiliaries.R (try_as): new utility
572 :     * R/sparseMatrix.R: use try_as() in coercion to original class
573 :    
574 : maechler 956 2005-09-30 Martin Maechler <maechler@stat.math.ethz.ch>
575 :    
576 :     * src/dgCMatrix.c (double_to_csc): and dgeMatrix_to_csc()
577 :    
578 :     2005-09-29 Martin Maechler <maechler@stat.math.ethz.ch>
579 :    
580 :     * R/Auxiliaries.R (dimNamesCheck): added
581 :    
582 :     * R/Matrix.R (as.array), (as.vector): new
583 :    
584 : maechler 954 2005-09-28 Martin Maechler <maechler@stat.math.ethz.ch>
585 :    
586 :     * R/Matrix.R (Matrix): get logical argument 'sparse' with a smart
587 : maechler 956 default.
588 :     * R/AllClass.R: move 'factors' slot toplevel "Matrix";
589 :     "pMatrix" now contains "sparseMatrix"
590 : maechler 954
591 : maechler 948 2005-09-26 Martin Maechler <maechler@stat.math.ethz.ch>
592 :    
593 :     * tests/Class+Meth.R: new tests; t(t(m)) == m
594 :    
595 :     * src/dtCMatrix.c (tsc_transpose): add forgotten "diag" slot
596 :    
597 :     * src/dsTMatrix.c (dsTMatrix_as_dsCMatrix): bad typo (segfault!)
598 :     * src/dtTMatrix.c (dtTMatrix_as_dtCMatrix): new
599 :    
600 :     * R/dspMatrix.R: typo in "t" method
601 :    
602 : maechler 925 2005-09-18 Douglas Bates <bates@wisc.edu>
603 :    
604 :     * R/AllClass.R (TsparseMatrix), CsparseM* and RsparseM*
605 :     * R/Tsparse.R: instead of R/gTMatrix.R
606 :     * R/Csparse.R: new
607 :     * src/Tsparse.c (Tsparse_to_Csparse): new; -> cholmod_()
608 :     * src/Tsparse.c: new; many trivial methods calling cholmod_()
609 :     * src/Csparse.c (Csparse_to_Tsparse), transpose, (mat|cross)prod:
610 :     via cholmod
611 :    
612 :     2005-09-16 Martin Maechler <maechler@stat.math.ethz.ch>
613 :    
614 :     * R/Auxiliaries.R (non0ind): new function using new C code
615 :     * src/dgCMatrix.c (compressed_non_0_ij): new utility
616 :    
617 : bates 917 2005-09-15 Douglas Bates <bates@localhost.localdomain>
618 :    
619 :     * src/chm_common.h: header file required by all C sources that
620 : maechler 1174 call CHOLMOD functions. It defines a cholmod_common structure
621 : bates 917 called 'c' whose address is passed as the last argument to
622 :     (virtually) every CHOLMOD function.
623 :    
624 :     * src/Pattern.c: Simple example of the use of CHOLMOD.
625 :    
626 :     * src/init.c: initialize and finalize the cholmod_common structure.
627 :    
628 :     * src/Makefile: Added source packages CHOLMOD UMFPACK AMD COLAMD
629 :     LDL and CCOLAMD from the U. of Florida sparse matrix library.
630 :    
631 : maechler 908 2005-09-08 Martin Maechler <maechler@stat.math.ethz.ch>
632 :    
633 :     * inst/test-tools.R: new file collecting the utility functions used
634 :     in ./tests/*.R
635 :    
636 :     * R/ddenseMatrix.R (cbind2): new methods for "numeric" and "matrix"
637 :     * R/Matrix.R (cbind2): methods for NULL and missing
638 :    
639 : maechler 886 2005-08-31 Martin Maechler <maechler@stat.math.ethz.ch>
640 :    
641 :     * R/AllClass.R: new "index" class for "[" and "[<-":
642 :     First cut at "symmetricMatrix" and "triangularMatrix"
643 :     * R/gTMatrix.R (.ind.prep): new function;
644 : maechler 1174 Logical and character indexing now work too.
645 : maechler 886 * R/Matrix.R: cheap "[<-" methods for denseMatrix now work
646 :     * tests/indexing.R: new, including *.Rout.save
647 :     * tests/dgTMatrix.R: new
648 :    
649 : bates 876 2005-08-29 Douglas Bates <bates@wisc.edu>
650 :    
651 :     * src/dgTMatrix.c (graphNEL_as_dgTMatrix): Corrected the position
652 :     indicator pos not being updated. Also enforced upper triangular
653 :     for symmetric case. Need to coerce edges component of elements of
654 :     edge list - grr! (Why don't they define their classes cleanly?)
655 :    
656 : maechler 871 2005-08-26 Martin Maechler <maechler@stat.math.ethz.ch>
657 :    
658 :     * R/Matrix.R: added first "[<-" methods; not yet functional
659 : bates 1352 * R/denseMatrix.R: ditto
660 : maechler 871 * man/Subassign-methods.Rd: new help file for these
661 :    
662 :     2005-08-25 Martin Maechler <maechler@stat.math.ethz.ch>
663 :    
664 :     * DESCRIPTION (Version): 0.98-6
665 :    
666 :     * R/denseMatrix.R: new file for "[" fallback methods for all dense
667 :     matrices.
668 :    
669 : maechler 868 2005-08-19 Martin Maechler <maechler@stat.math.ethz.ch>
670 :    
671 :     * src/lgCMatrix.c (lcsc_to_matrix): new; need for
672 :     as( <logical>, "matrix")
673 :    
674 :     * R/pMatrix.R: coercion to "lgTMatrix"
675 :    
676 :     * R/gTMatrix.R: new virtual class to define "[" methods for.
677 :     * man/gTMatrix-class.Rd:
678 :     * General slight re-organization of where "[" methods are defined.
679 :     more to come.
680 :    
681 : maechler 871 2005-08-18 Douglas Bates <bates@wisc.edu>
682 : maechler 868
683 : maechler 1174 * DESCRIPTION (Version): 0.98-5 released to CRAN
684 : maechler 871
685 :     * src/dgTMatrix.c (graphNEL_as_dgTMatrix): add first graphNEL methods
686 :     * .....
687 :    
688 : bates 863 2005-08-18 Douglas Bates <bates@localhost.localdomain>
689 :    
690 :     * R/lmer.R: Corrected naming scheme in mcmcsamp to work with lmer
691 :     or glmer objects.
692 :    
693 : maechler 860 2005-08-17 Martin Maechler <maechler@stat.math.ethz.ch>
694 :    
695 :     * DESCRIPTION (Version): 0.98-4 : upload to CRAN
696 :    
697 :     2005-08-16 Douglas Bates <bates@localhost.localdomain>
698 :    
699 :     * R/HBMM.R: finish re-writing R-only code.
700 :    
701 : bates 854 2005-08-15 Douglas Bates <bates@localhost.localdomain>
702 :    
703 :     * man/externalFormats.Rd: move documentation for writeHB and
704 :     writeMM here.
705 :    
706 :     * src/mmio.c: replace inclusion of <malloc.h> by <stdlib.h>
707 :     (suggested by Paul Roecker).
708 :    
709 :     * tests/validObj.R (assertError): Comment out test that is failing
710 :     after recent changes in r-devel.
711 :    
712 : maechler 860
713 : maechler 848 2005-08-11 Martin Maechler <maechler@stat.math.ethz.ch>
714 :    
715 :     * R/AllClass.R: intermediate virtual class "denseMatrix"
716 :     * man/denseMatrix-class.Rd
717 :     * NAMESPACE: export it, and also export
718 :     * man/unused-classes.Rd: "iMatrix", "zMatrix" and "ldenseMatrix"
719 :    
720 : bates 846 2005-08-10 Douglas Bates <bates@wisc.edu>
721 :    
722 : maechler 848 * DESCRIPTION (Version): 0.98-3 to CRAN
723 :    
724 : bates 846 * src/dtrMatrix.c (dtrMatrix_validate): fixed up validation and
725 :     matrix_solve code (which was really, really wrong).
726 :    
727 : bates 835 2005-08-07 Douglas Bates <bates@wisc.edu>
728 : maechler 834
729 :     * DESCRIPTION (Version): 0.98-2
730 :    
731 :     * R/HBMM.R (readHB), (readMM): read Matrix Market formats
732 :    
733 :     * R/lmer.R (abbrvNms): new
734 :     * R/lmer.R (mcmcsamp): allow transformed parameters
735 : bates 835 * src/HBMM.c (Matrix_writeMatrixMarket): Added read/write routines
736 :     for the Harwell-Boeing and the MatrixMarket formats.
737 : maechler 834
738 :     2005-08-04 Martin Maechler <maechler@stat.math.ethz.ch>
739 :    
740 :     * man/dtrMatrix-class.Rd: add examples
741 : bates 835 * man/dtpMatrix-class.Rd: ditto; plus note about PROBLEM
742 : maechler 834
743 :     * TODO: note the dtpMatrix (docu) bug
744 :    
745 :     * R/zzz.R (.onLoad): assignInNamespace("as.matrix", *, "base")
746 :     in order to ensure that new as.matrix() is used by old functions,
747 :     e.g., svd(), qr(), eigen(), dist(),..;
748 :     apply(), also matplot() or pairs().
749 :    
750 :    
751 :     2005-08-03 Martin Maechler <maechler@stat.math.ethz.ch>
752 :    
753 :     * R/lmer.R: add 'fixme' comments and move the linear vs glm check;
754 :     add comments about 'control' / lmerControl() arguments
755 :    
756 : bates 835 2005-07-27 Douglas Bates <bates@wisc.edu>
757 : bates 820
758 : bates 835 * man/sleepstudy.Rd: Added the sleep data set.
759 : maechler 1174 * DESCRIPTION (Version): 0.98-1 released to CRAN
760 : bates 820
761 : bates 835 2005-07-12 Douglas Bates <bates@wisc.edu>
762 : maechler 834 * man/sleepstudy.Rd: Added the sleep data set.
763 :    
764 : bates 809 * R/lmer.R (glmmMCMC): Added PACKAGE = "Matrix" in a couple of
765 :     .Call calls that were producing spurious output.
766 :    
767 : bates 835 2005-07-05 Douglas Bates <bates@wisc.edu>
768 : bates 801
769 :     * R/lmer.R (lmer): stored updated variance component estimates in
770 :     mer object for the generalized model. (Bug reported by Renaud
771 :     Lancelot).
772 :    
773 : bates 835 2005-07-03 Douglas Bates <bates@wisc.edu>
774 : bates 794
775 :     * src/lmer.c (glmer_devAGQ): Added AGQ for single grouping factor,
776 :     unidimensional case.
777 :    
778 : bates 835 2005-06-08 Douglas Bates <bates@wisc.edu>
779 : maechler 791
780 :     * DESCRIPTION (Version): 0.96-1
781 :    
782 : maechler 1174 * moved lmer-class' R and C code moved from lme4 to here
783 : maechler 791
784 : bates 835 2005-06-04 Douglas Bates <bates@wisc.edu>
785 : bates 763
786 :     * R/dgCMatrix.R: Call to csc_matrix_mm used undefined arguments
787 :     (reported by Guissepe Ragusa <gragusa@ucsd.edu>)
788 :    
789 : bates 835 2005-06-02 Douglas Bates <bates@wisc.edu>
790 : bates 763
791 :     * src/Makefile.win: Forgot to update this when Makefile changed.
792 :    
793 : bates 835 2005-05-11 Douglas Bates <bates@wisc.edu>
794 : bates 726
795 :     * src/dgCMatrix.c (csc_transpose): Simplified function fixing a
796 :     bug reported by Kurt Hornik and Michael Hahsler.
797 :    
798 : bates 835 2005-05-10 Douglas Bates <bates@wisc.edu>
799 : bates 725
800 :     * src/lgCMatrix.c (Matrix_lgClgCmm): Implementation of methods for
801 :     logical sparse matrices. These will also be used in the symbolic
802 :     analysis for lmer objects.
803 :    
804 :     * src/dsCMatrix.c (dsCMatrix_matrix_solve): Copied the dimensions
805 :     of b to the result. Fixes bug reported by Jean.Coursol@math.u-psud.fr
806 : maechler 791
807 : bates 835 2005-05-06 Douglas Bates <bates@wisc.edu>
808 : bates 714
809 :     * src/dgeMatrix.c (dgeMatrix_colsums): Added an implementation of
810 :     colMeans, colSums, rowMeans and rowSums.
811 :    
812 : bates 835 2005-04-18 Douglas Bates <bates@wisc.edu>
813 : bates 692
814 :     * src/lgCMatrix.[ch]: code for _validate method and stub for
815 :     multiplication operation.
816 :    
817 :     * src/dgeMatrix.c (dgeMatrix_matrix_solve): Passing wrong argument
818 :     to dgetrs.
819 :    
820 :     * src/init.c: Fix cut-and-paste error in definition of
821 :     dgeMatrix_matrix_solve
822 :    
823 :     * src/{many files}: Tighten code by using ALLOC_SLOT.
824 :    
825 : bates 835 2005-04-15 Douglas Bates <bates@wisc.edu>
826 : bates 692
827 :     * R/AllClass.R: Add lgTMatrix and lgCMatrix classes
828 :    
829 :     * DESCRIPTION: Eliminate import of stats.
830 :    
831 : maechler 791
832 : bates 835 2005-04-06 Douglas Bates <bates@wisc.edu>
833 : bates 692
834 :     * R/AllClass.R : add logical sparse matrix classes
835 :    
836 : maechler 687 2005-04-01 Martin Maechler <maechler@stat.math.ethz.ch>
837 :    
838 :     * R/dgTMatrix.R: add "[" method for triplet matrices
839 :     * R/sparseMatrix.R: and other sparse ones; --> add show() for sparse
840 :    
841 : bates 835 2005-03-31 Douglas Bates <bates@wisc.edu>
842 : maechler 687
843 :     * DESCRIPTION (Version): release 0.95-5 to CRAN
844 :    
845 :     * R/dMatrix.R: add %*%, crossprod and solve "fallback" methods
846 :     * R/sparseMatrix.R: %*%, crossprod()
847 :     * R/dgeMatrix.R: more "fallback" methods for numeric/dense matrices
848 :     * man/*.Rd: move method definitions to 'Matrix' and 'dMatrix'
849 :     * src/lmer.c (lmer_fitted): fix thinko
850 :    
851 : maechler 676 2005-03-26 Martin Maechler <maechler@stat.math.ethz.ch>
852 :    
853 :     * R/AllClass.R: add two virtual sparse classes ``on top''
854 :    
855 :     2005-03-24 Martin Maechler <maechler@stat.math.ethz.ch>
856 :    
857 :     * R/AllClass.R (setClass): use "VIRTUAL" for the virtual classes;
858 :     correspondingly fix examples and tests/ since new()
859 :     doesn't work for virtual classes.
860 :    
861 : maechler 658 2005-03-17 Martin Maechler <maechler@stat.math.ethz.ch>
862 :    
863 :     * R/Matrix.R (as.matrix): method and one for unname()
864 :     * tests/dpoMatrix.R: tests should now be less platform dependent;
865 :     also run for R 2.1.0; using as.matrix()
866 :    
867 : bates 835 2005-03-15 Douglas Bates <bates@wisc.edu>
868 : maechler 658
869 :     * R/pMatrix.R: "pMatrix" class added
870 :     * ....
871 :    
872 : bates 835 2005-03-14 Douglas Bates <bates@wisc.edu>
873 : bates 645
874 :     * R/dtpMatrix.R: Add unpack method and an example.
875 :    
876 :     * src/dsyMatrix.c (dsyMatrix_trf): Add BunchKaufman factorization
877 :     of general symmetric matrices and associated S4 methods.
878 :    
879 : maechler 658 2005-03-10 Martin Maechler <maechler@stat.math.ethz.ch>
880 :     +
881 :     2005-03-05 Martin Maechler <maechler@stat.math.ethz.ch>
882 :    
883 :     * R/dgeMatrix.R (setAs): and many other files: more coercion,
884 :     crossprod() and "%*%" methods added; tests, too.
885 :     * tests/matprod.R: new, for testing these
886 :    
887 : bates 835 2005-03-03 Douglas Bates <bates@wisc.edu>
888 : bates 599
889 :     * src/lmer.c (lmer_fitted): Added.
890 :    
891 : bates 835 2005-03-02 Douglas Bates <bates@wisc.edu>
892 : bates 596
893 :     * R/dsTMatrix.R: Conversion from dsTMatrix to dsCMatrix
894 :    
895 : bates 835 2005-02-28 Douglas Bates <bates@wisc.edu>
896 : bates 582
897 :     * src/*.c,po/,inst/po: Internationalization and localization of
898 :     the package.
899 :    
900 :     * src/ldl.[ch]: Removed these as their contents are referenced in the
901 :     R_ldl.c file.
902 :    
903 :     * src/flame.[ch]: Removed these source files.
904 : maechler 658
905 : bates 582 * src/dtrMatrix.c (make_array_triangular): Move to Mutils
906 :    
907 :     * src/LU.[ch],src/init.c: absorb in factorizations
908 :    
909 :     * src/Mutils.h: prepare for internationalization
910 :    
911 :     * src/cblas.h: move the enum definitions to Mutils.h and remove
912 :     this file
913 :    
914 : maechler 578 2005-02-26 Martin Maechler <maechler@stat.math.ethz.ch>
915 :    
916 : maechler 579 * R/dgeMatrix.R: provide "dimnames" and "dimnames<-" methods
917 :    
918 :     * R/dtrMatrix.R: fix t() method
919 :    
920 : maechler 578 * R/dgeMatrix.R: define group methods "Arith", "Math", "Math2"
921 : maechler 658 * NAMESPACE: export them (and import generics from "methods")
922 : maechler 578 * tests/group-methods.R : and test them.
923 :    
924 :     * src/dtrMatrix.c (dtrMatrix_as_dgeMatrix): prevent seg.fault in
925 :     border case
926 :    
927 :     2005-02-24 Douglas Bates <bates@stat.wisc.edu>
928 :    
929 : maechler 658 * DESCRIPTION (Version): 0.95-2 released to CRAN
930 : maechler 578
931 :     * src/dgBCMatrix.c:
932 :     * src/lmer.c: many changes
933 :     * ...
934 :    
935 : maechler 512 2005-02-04 Martin Maechler <maechler@stat.math.ethz.ch>
936 :    
937 :     * R/Matrix.R: add more sophisticated show() method.
938 :    
939 : maechler 578 2005-02-02 Douglas Bates <bates@stat.wisc.edu>
940 :    
941 :     * */* : almost complete reorganization of classes.
942 :    
943 : bates 835 2005-01-26 Douglas Bates <bates@wisc.edu>
944 : bates 460
945 :     * R/AllGeneric.R: Added matrix exponential generic expm and a method
946 :     for the geMatrix class.
947 :    
948 : bates 835 2005-01-24 Douglas Bates <bates@wisc.edu>
949 : bates 460
950 :     * src/Makefile (clean): Remove *.a and *.so
951 :    
952 :     * man/cscBlocked-class.Rd: Remove reference to the lmer-class.
953 :    
954 : bates 835 2005-01-23 Douglas Bates <bates@wisc.edu>
955 : bates 460
956 : maechler 658 * src/lmer.c (Lind): Definition of Lind was backwards. This only
957 : bates 460 had an effect in cases with more than 2 grouping factors.
958 :    
959 : bates 835 2005-01-03 Douglas Bates <bates@wisc.edu>
960 : bates 415
961 :     * src/lmeRep.c (lmer_variances): change from lmeRep to lmer
962 :    
963 : bates 835 2004-12-23 Douglas Bates <bates@wisc.edu>
964 : bates 410
965 :     * src/init.c (R_init_Matrix): Reorder calls to R_registerRoutines
966 :     and R_useDynamicSymbols (suggested by B.D.Ripley).
967 :    
968 : bates 835 2004-12-14 Douglas Bates <bates@wisc.edu>
969 : bates 392
970 :     * R/sscMatrix.R: Add determinant methods
971 :    
972 :     * src/triplet.[ch],src/init.c (triplet_to_matrix): Add a coercion
973 :     for tripletMatrix to matrix.
974 :    
975 : bates 835 2004-12-13 Douglas Bates <bates@wisc.edu>
976 : bates 388
977 : bates 392 * R/AllClass.R (.onLoad): Eliminate the bbCrosstab class, which is
978 :     no longer used.
979 :    
980 : bates 388 * src/R_ldl.c: Created an R-specific version of the ldl.[ch] files
981 :     with dynamic allocation of scratch arrays.
982 :    
983 :     * src/ssclme.c (ssclme_copy_ctab): Fixed bug in creation of ZtZ
984 :     for multivariate random effects with multiple grouping factors.
985 :     Fixes part but not all of #15.
986 :    
987 : bates 835 2004-12-03 Douglas Bates <bates@wisc.edu>
988 : bates 375
989 :     * src/lmeRep.c (lmeRep_factor): order of operations for multiple
990 :     scalar grouping factors corrected.
991 :    
992 : bates 835 2004-11-29 Douglas Bates <bates@wisc.edu>
993 : bates 375
994 :     * src/bCrosstab.c: remove diag_update which is no longer used
995 :    
996 : bates 835 2004-11-16 Douglas Bates <bates@wisc.edu>
997 : bates 350
998 :     * src/Metis_utils.c: Move metis.h include to C sources so that the
999 :     .h file can be included.
1000 :    
1001 : bates 835 2004-11-12 Douglas Bates <bates@wisc.edu>
1002 : bates 342
1003 : bates 350 * src/LU.c,geMatrix.c,trMatrix.c, etc.:
1004 : bates 342 Complete allocation of slots in NEW_OBJECT.
1005 :    
1006 :     * src/Mutils.h: Moved list of symbols to an include file
1007 :    
1008 : bates 835 2004-11-11 Douglas Bates <bates@wisc.edu>
1009 : bates 342
1010 :     * src/geMutils.c (Matrix_init): remove unused function
1011 :    
1012 : bates 835 2004-11-10 Douglas Bates <bates@wisc.edu>
1013 : bates 342
1014 :     * src/cscMatrix.c (csc_to_imagemat): removed unused function
1015 :    
1016 : bates 835 2004-11-05 Douglas Bates <bates@wisc.edu>
1017 : bates 327
1018 :     * src/Makefile.win (SOURCES_C): Keep consistent with Makefile
1019 :    
1020 : bates 835 2004-10-27 Douglas Bates <bates@wisc.edu>
1021 : bates 303
1022 :     * R/pdmatrix.R: remove PACKAGE="Matrix" in .Call calls
1023 :    
1024 : bates 835 2004-10-04 Douglas Bates <bates@wisc.edu>
1025 : bates 296
1026 :     * src/init.c: Created R_init_Matrix and added registration of C
1027 :     routines.
1028 :    
1029 : bates 835 2004-10-02 Douglas Bates <bates@wisc.edu>
1030 : bates 283
1031 :     * R/tripletMatrix.R: Force a require(lattice) for the image methods.
1032 :    
1033 : bates 835 2004-06-15 Douglas Bates <bates@wisc.edu>
1034 : bates 229
1035 :     * man/trMatrix-class.Rd: Escape the % chars in .Rd files.
1036 :    
1037 : bates 111 2004-04-20 Douglas Bates <bates@stat.wisc.edu>
1038 :    
1039 :     * src/Makefile.win ($(SHLIB)): Modifications per Uwe Ligges.
1040 :    
1041 : bates 109 2004-04-19 Douglas Bates <bates@stat.wisc.edu>
1042 :    
1043 :     * src/ssclme.c (ssclme_update_mm): fix logic error in
1044 :     ssclme_update_mm
1045 :    
1046 : bates 105 2004-04-18 Douglas Bates <bates@stat.wisc.edu>
1047 :    
1048 :     * src/ssclme.c (ssclme_coef, ssclme_coefGets): Create consistency
1049 :     in the order of unconstrained and constrained parameters.
1050 :     (ssclme_gradient): Added the gradients (not yet correct for
1051 :     multidimensional, unconstrained case).
1052 :    
1053 : bates 78 2004-04-14 Douglas Bates <bates@stat.wisc.edu>
1054 :    
1055 :     * src/ssclme.c (ssclme_EMsteps): Fix logic in REML update
1056 :    
1057 :     * src/Makefile.win: Remove unneeded ranlib call
1058 :    
1059 : bates 71 2004-04-12 Douglas Bates <bates@stat.wisc.edu>
1060 :    
1061 :     * DESCRIPTION (Version): New release
1062 :    
1063 :     * src/Makefile.win: Update Makefile.win to umfpack removal.
1064 :    
1065 : bates 49 2004-04-05 Douglas Bates <bates@bates2_home>
1066 :    
1067 :     * src/triplet_to_col.c: Create triplet_to_col as a native
1068 : maechler 658 function, not the version from umfpack. There were problems with
1069 : bates 49 the configuration of UMFPACK for 64-bit processors and there was
1070 :     only one umfpack routine being used so I moved it here.
1071 :    
1072 : bates 45 2004-04-04 Douglas Bates <bates@bates2_home>
1073 :    
1074 :     * src/ssclme.c (ssclme_variances): New function.
1075 :    
1076 : bates 28 2004-03-28 Douglas Bates <bates@bates2_home>
1077 :    
1078 :     * src/ssclme.c (ssclme_fitted): Added function.
1079 :    
1080 : bates 22 2004-03-27 Douglas Bates <bates@bates2_home>
1081 :    
1082 :     * src/ssclme.c (ssclme_transfer_dimnames): Add new function to
1083 :     store the dimnames in the XtX and bVar slots
1084 :     (ssclme_update_mm): Change the dimensions of the bVar slot
1085 :     components and the returned value from ssclme_ranef.
1086 :    
1087 : bates 10 2004-03-18 Douglas Bates <bates@stat.wisc.edu>
1088 :    
1089 :     * R/{pdMat.R,pdIdent.R,pdLogChol.R,pdMatrixLog.R,pdNatural.R},
1090 :     src/{pdMat.c,pdIdent.c,pdLogChol.c,pdNatural.c},
1091 :     tests/{pdCompSymm.R,pdDiag.R,pdIdent.R,pdLogChol.R,pdNatural.R},
1092 :     man/{pdMat-class.Rd,pdmatrix-class.Rd,corrmatrix-class.Rd,
1093 :     pdDiag-class.Rd,pdIdent-class.Rd,pdNatural-class.Rd,
1094 :     pdLogChol-class.Rd,coefGets.Rd,pdCompSymm-class.Rd,
1095 :     pdfactor-class.Rd,pdFactor.Rd,pdMatrix.Rd,
1096 :     pdBlocked-class.Rd},AllClass.R,AllGeneric.R:
1097 :     Moved the pdMat classes from the lme4 package.
1098 :    
1099 :     2004-03-02 Douglas Bates <bates@stat.wisc.edu>
1100 :    
1101 :     * man/ssclme-class.Rd: Update definition and documentation of the
1102 :     ssclme class to include the DIsqrt slot.
1103 :    
1104 :     * src/ssclme.c (ssclme_deviance): Modify order of computation
1105 :     (much faster using dsyrk, a level 3 BLAS routine).
1106 :    
1107 :     * src/Makefile (SUBLIBS): Change definition (K. Hornik)
1108 :    
1109 :     2004-02-28 Douglas Bates <bates@stat.wisc.edu>
1110 :    
1111 :     * tests/ssclme.R: Modify the test to account for the permutation
1112 :     of the levels of the grouping factors.
1113 :    
1114 :     2004-02-23 Douglas Bates <bates@stat.wisc.edu>
1115 :    
1116 :     * R/ssclme.R,src/ssclme.c (ssclme): Move slots of sscCrosstab slot
1117 :     directly into the ssclme class definition.
1118 :    
1119 :     2004-02-22 Douglas Bates <bates@stat.wisc.edu>
1120 :    
1121 :     * DESCRIPTION (Date): New release
1122 :    
1123 :     * man/ssclme-class.Rd: new file.
1124 :    
1125 :     * src/ssclme.c (ssclme_loglik): major revisions in design. It
1126 :     works and it's fast!
1127 :    
1128 :     2004-02-17 Douglas Bates <bates@stat.wisc.edu>
1129 :    
1130 :     * src/taucs/Makefile.win (lib): Change "ar" to "$(AR)" (B.Ripley)
1131 :    
1132 :     2004-02-16 Douglas Bates <bates@stat.wisc.edu>
1133 :    
1134 :     * DESCRIPTION (Date): New release
1135 :    
1136 :     * NAMESPACE: Don't export ssclme.
1137 :    
1138 :     * data/ScotsSec.rda, man/ScotsSec.Rd: Add Scottish secondary
1139 :     school data.
1140 :    
1141 :     2004-02-11 Douglas Bates <bates@stat.wisc.edu>
1142 :    
1143 :     * src/sscCrosstab.c (sscCrosstab): Added a row to the incidence to
1144 :     keep track of the fixed-effects and the response. Counts also
1145 :     gets an extra element, which is always one.
1146 :    
1147 :     * src/ldl.c: Include these routines from Tim Davis' LDL package.
1148 :    
1149 :     2004-02-10 Douglas Bates <bates@stat.wisc.edu>
1150 :    
1151 :     * src/cscMatrix.c (csc_transpose): new function
1152 :    
1153 :     * src/Mutils.c (csc_sort_columns): perm/iperm confusion corrected
1154 :     (csc_components_transpose): new function
1155 :    
1156 :     2004-02-06 Douglas Bates <bates@stat.wisc.edu>
1157 :    
1158 :     * src/triplet.c (triplet_validate): Fix Dim slot on generated
1159 :     triplets
1160 :    
1161 :     2004-01-30 Douglas Bates <bates@stat.wisc.edu>
1162 :    
1163 :     * R/sscCrosstab.R (sscCrosstab): Added sscCrosstab generator function.
1164 :    
1165 :     * src/LU.h (MATRIX_LU_H): Add #ifndef #define ... #endif to this
1166 :     and all other .h files in src.
1167 :    
1168 :     * src/Makefile.win: This and other Makefile.win files contributed
1169 :     by Brian Ripley.
1170 :    
1171 :     2004-01-27 Douglas Bates <bates@stat.wisc.edu>
1172 :    
1173 :     * R/syMatrix.R: Added methods for "%*%".
1174 :    
1175 :     * R/Hilbert.R (Hilbert): Changed Hilbert function to return a
1176 :     poMatrix object.
1177 :    
1178 :     2004-01-26 Douglas Bates <bates@stat.wisc.edu>
1179 :    
1180 :     * man/sscChol-class.Rd,man/mm.Rd,man/y.Rd: Added man pages.
1181 :    
1182 :     2004-01-25 Douglas Bates <bates@bates2_home>
1183 :    
1184 :     * inst/doc/Introduction.Rnw,Comparisons.Rnw: Added vignettes.
1185 :    
1186 :     * R/csc.R: Convert all cscMatrix classes to use Dim slot instead
1187 :     of nrow.
1188 :    
1189 :     2003-12-31 Douglas Bates <bates@stat.wisc.edu>
1190 :    
1191 :     * src/taucs/taucs.h: Moved taucs.h, amd.h, and umfpack.h into
1192 :     subdirectories.
1193 :    
1194 :     2003-12-08 Douglas Bates <bates@stat.wisc.edu>
1195 :    
1196 :     * src/taucs.h: Accidently referred to global header files
1197 :     instead of local files.
1198 :    
1199 :     2003-12-04 Douglas Bates <bates@stat.wisc.edu>
1200 :    
1201 :     * R/AllClass.R: Lots of changes. Removed all the lapack++ code
1202 :     and methods and replaced all classes with S4 classes.
1203 :    
1204 :     2003-04-19 Douglas Bates <bates@stat.wisc.edu>
1205 :    
1206 :     * R/det.R,man/det.Rd: Change name of det generic to determinant
1207 :    
1208 :     * src/R_LapackPP.cc: Change method of calculating determinants
1209 :    
1210 :     2003-02-03 Douglas Bates <bates@stat.wisc.edu>
1211 :    
1212 :     * DESCRIPTION (Version): removed empty data directory as requested
1213 :     by CRAN maintainers. Changed version number and date.
1214 :    
1215 :     2002-10-23 Douglas Bates <bates@stat.wisc.edu>
1216 :    
1217 :     * src/laindex.h: Applied patches from Brian Ripley for compilation
1218 :     under Windows.
1219 :    
1220 :     * Added configure.win and src/Makevars.win as requested by Brian
1221 :     Ripley.
1222 :    
1223 :     2002-05-03 Douglas Bates <bates@stat.wisc.edu>
1224 :    
1225 :     * src/lamatrix.h: Removing pre-1.2.0 compatibility code per Kurt
1226 :     Hornik.
1227 :    
1228 :     2002-04-24 Douglas Bates <bates@stat.wisc.edu>
1229 :    
1230 :     * configure.ac: Replaced configure.in with configure.ac
1231 :     contributed by Kurt Hornik.
1232 :    
1233 :     * aclocal.m4 (ac_clean_files): Replaced this with Kurt Hornik's
1234 :     version for R-1.5.0
1235 :    
1236 : maechler 512
1237 : bates 10 2001-12-10 Douglas Bates <bates@stat.wisc.edu>
1238 :    
1239 :     * man/eigen.Rd: Removed the .Alias in the example

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