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Annotation of /pkg/ChangeLog

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1 : maechler 1883 2007-06-06 Martin Maechler <maechler@stat.math.ethz.ch>
2 :    
3 :     * R/lsparseMatrix.R, R/ldenseMatrix.R (all, any): change default to
4 :     'na.rm = FALSE' as "everywhere" else in R.
5 :    
6 : bates 1877 2007-06-05 Douglas Bates <bates@stat.wisc.edu>
7 :    
8 : bates 1878 * [r4421] src/CSparse_install.sh: Modify for new organization of
9 : maechler 1883 CSparse package
10 : bates 1877 * [r4425] src/UFsparse_download.sh: Update to version 3.0.0 of
11 :     SuiteSparse
12 :     * [r4426] src/Makefile: add ./UFconfig to the include path for
13 :     compilation
14 : maechler 1883 * [r4427] src/cs.[ch]: update to CSparse version 2.2.0
15 :     * [r4428] inst/doc/UFsparse/* src/{AMD,CHOLMOD,COLAMD}/*
16 :     src/UFconfig/UFconfig.h: Update to version 3.0.0 of SuiteSparse
17 :    
18 : maechler 1870 2007-06-05 Martin Maechler <maechler@stat.math.ethz.ch>
19 :    
20 :     * R/Auxiliaries.R (emptyColnames): + argument msg.if.not.empty, used in
21 :     * R/sparseMatrix.R (prSpMatrix): now gives a message about
22 :     suppressed column names.
23 :    
24 : bates 1868 2007-06-04 17:13 Douglas Bates <bates@stat.wisc.edu>
25 :    
26 :     * [r4418] src/Csparse.c, src/HBMM.c, src/Mutils.c, src/Mutils.h,
27 :     src/Tsparse.c, src/chm_common.c, src/chm_common.h, src/dgCMatrix.c,
28 :     src/dgeMatrix.c, src/dpoMatrix.c, src/dpoMatrix.h, src/dppMatrix.c,
29 :     src/dppMatrix.h, src/dsCMatrix.c, src/dspMatrix.c, src/dspMatrix.h,
30 :     src/dsyMatrix.c, src/dsyMatrix.h, src/dtpMatrix.c, src/dtrMatrix.c:
31 :     Remove warnings after change to const char* CHAR
32 :    
33 :     2007-06-04 17:11 Douglas Bates <bates@stat.wisc.edu>
34 :    
35 :     * [r4417] inst/include/Matrix_stubs.c, inst/include/cholmod.h: Corrected
36 :     type of M_cholmod_ssmult
37 :    
38 : bates 1863 2007-06-03 14:42 Douglas Bates <bates@stat.wisc.edu>
39 :    
40 :     * [r4412] inst/include/Matrix_stubs.c, inst/include/cholmod.h,
41 :     src/init.c: Yet another cholmod export - cholmod_ssmult
42 :    
43 : maechler 1855 2007-05-23 Martin Maechler <maechler@stat.math.ethz.ch>
44 :    
45 :     * NAMESPACE: exported drop0(), since
46 :     * man/drop0.Rd: I have seen several cases, I really wanted to use
47 :     it, so our users may want too.
48 :    
49 :     2007-05-22 Martin Maechler <maechler@stat.math.ethz.ch>
50 :    
51 :     * man/colSums.Rd: separately document colSums() etc, since these
52 :     have the extra argument 'sparseResult'.
53 :    
54 : maechler 1852 2007-05-21 Martin Maechler <maechler@stat.math.ethz.ch>
55 :    
56 :     * R/sparseMatrix.R (spMatrix): utility (T)sparse Matrix constructor;
57 :     * man/spMatrix.Rd: docu., including examples
58 :    
59 :     * R/Auxiliaries.R (sp.colMeans): etc, using a patched callGeneric(),
60 :     in order to make colMeans() etc fast *and* correct.
61 :     * R/sparseVector.R (replSPvec): "[<-" functionality for
62 :     sparseVectors; tested in
63 :     * tests/simple.R:
64 :    
65 :     2007-05-19 Martin Maechler <maechler@stat.math.ethz.ch>
66 :    
67 :     * R/sparseMatrix.R (print.sparseSummary): and summary() method for
68 :     (very) sparse Matrices; output similar to Matlab's print().
69 :    
70 : bates 1847 2007-05-17 Douglas Bates <bates@stat.wisc.edu>
71 :    
72 :     * src/HBMM.c (Matrix_writeMatrixMarket): Write 1-based, not
73 :     0-based, indices (Jose Quesada <quesada@gmail.com>).
74 :    
75 : bates 1844 2007-05-16 Douglas Bates <bates@stat.wisc.edu>
76 :    
77 :     * R/CHMfactor.R: Added solve methods for a CHMfactor object.
78 :    
79 : maechler 1845 2007-05-16 Martin Maechler <maechler@stat.math.ethz.ch>
80 :    
81 :     * R/Auxiliaries.R (sparsapply): new utility, much faster than
82 :     tapply1() for large sparse matrices.
83 :    
84 :     2007-05-15 Martin Maechler <maechler@stat.math.ethz.ch>
85 :    
86 :     * R/Matrix.R (dim<-): reshape now via sparseVector.
87 :    
88 :     * R/sparseVector.R: methods and function for
89 :     * R/AllClass.R: new "sparseVector" class and daughters.
90 :     * NAMESPACE: export new classes
91 :    
92 : maechler 1837 2007-05-14 Martin Maechler <maechler@stat.math.ethz.ch>
93 :    
94 :     * DESCRIPTION (Version): 0.99875-1
95 :     * src/Makefile.win: also remove Lapack code from here (cf. 04-25).
96 :    
97 : maechler 1834 2007-05-11 Martin Maechler <maechler@stat.math.ethz.ch>
98 :    
99 :     * R/Tsparse.R ([, Tsparse): fix last case: *duplicated*, symmetric
100 :     indexing
101 :     * tests/indexing.R: test set for that.
102 :    
103 : maechler 1833 2007-05-08 Martin Maechler <maechler@stat.math.ethz.ch>
104 :    
105 :     * R/Tsparse.R (replTmat): fix the case of *duplicated* index
106 :     entries.
107 :     * tests/indexing.R(out): add regression test for it
108 :    
109 :     2007-04-30 Martin Maechler <maechler@stat.math.ethz.ch>
110 :    
111 :     * R/(l(dense|sparse))?Matrix.R (!): use 'x', not 'e1' as argument
112 :     name for "!" method definitions.
113 :    
114 : maechler 1829 2007-04-26 Martin Maechler <maechler@stat.math.ethz.ch>
115 :    
116 :     * R/Tsparse.R (intI): new utility, used for "[" :
117 :     Cleanup up there, and fixes for duplicated indices - more TODO!
118 :    
119 :     * tests/indexing.R(out): more tests
120 :    
121 : bates 1827 2007-04-25 Douglas Bates <bates@stat.wisc.edu>
122 :    
123 :     * DESCRIPTION,src/Makefile: require R>= 2.5.0 and remove Lapack
124 :     code that is now part of the R Lapack library.
125 : maechler 1829
126 : bates 1827 * src/init.c,inst/include/{Matrix_stubs.c,cholmod.h}:export
127 :     cholmod_factorize_p (used in lme4 for GLMMs and NLMMs).
128 :    
129 : maechler 1829 2007-04-21 Martin Maechler <maechler@stat.math.ethz.ch>
130 :    
131 :     * R/Matrix.R (image): method for all Matrices, not just sparse ones.
132 :    
133 :     2007-04-17 Martin Maechler <maechler@stat.math.ethz.ch>
134 :    
135 :     * R/Auxiliaries.R (tapply1): unname(.) -> colSums() etc don't end
136 :     up with extraneous names '0'...'<n-1>'
137 :    
138 : maechler 1825 2007-04-12 Martin Maechler <maechler@stat.math.ethz.ch>
139 :    
140 :     * R/dgTMatrix.R (mat2dgT): care about NAs
141 :    
142 :     2007-04-11 Martin Maechler <maechler@stat.math.ethz.ch>
143 :    
144 :     * R/kronecker.R: triangularity preserving methods
145 :    
146 : maechler 1803 2007-03-27 Martin Maechler <maechler@stat.math.ethz.ch>
147 :    
148 :     * R/kronecker.R: new file collecting kronecker() methods in one
149 :     place. Goal: become much faster!
150 :    
151 : maechler 1799 2007-03-23 Martin Maechler <maechler@stat.math.ethz.ch>
152 :    
153 :     * src/dtCMatrix.c (dtCMatrix_solve): use the new code from Kasper
154 :     Kristensen based cs_spsolve() instead of _lsolve & _usolve which
155 :     can be much faster.
156 :    
157 :     * tests/matprod.R: add regression tests for these (upper & lower).
158 :    
159 :     2007-03-19 Martin Maechler <maechler@stat.math.ethz.ch>
160 :    
161 :     * R/Matrix.R (diff): method for our Matrices.
162 :    
163 :     * R/sparseMatrix.R (isDiagonal): check dim()!
164 :    
165 :     2007-03-17 Martin Maechler <maechler@stat.math.ethz.ch>
166 :    
167 :     * R/Matrix.R (dim<-): new method for "reshape()" built on a
168 :     proposal from Tamas Papp.
169 :    
170 :     2007-03-16 Martin Maechler <maechler@stat.math.ethz.ch>
171 :    
172 :     * R/AllGeneric.R: remove all if(!isGeneric(.)) clauses
173 :    
174 :     * R/zzz.R (.onLoad, .onUnload): do *not* leave bind_activation(TRUE);
175 : maechler 1803 rather define and export cBind() and rBind() only.
176 :     --> useRs *must* change code that used to have cbind()/rbind() !!
177 : maechler 1799
178 : maechler 1803 * R/bind.R: change tests from cbind() to cBind() and similarly to rBind()
179 :     * R/bind.Rout.save: ditto
180 : maechler 1799
181 : bates 1787 2007-02-16 Douglas Bates <bates@r-project.org>
182 :    
183 :     * DESCRIPTION (Date, Version): 0.9975-11 with new date
184 :     * src/dgCMatrix.c (R_to_CMatrix, compressed_to_TMatrix): remove
185 :     const modifier on declaration of the array 'valid'
186 :    
187 : bates 1786 2007-02-12 Douglas Bates <bates@stat.wisc.edu>
188 :    
189 :     * R/CHMfactor.R: Add image method (coercion to sparseMatrix).
190 :    
191 : maechler 1765 2007-02-05 Martin Maechler <maechler@stat.math.ethz.ch>
192 :    
193 : maechler 1768 * DESCRIPTION (Date, Version): 0.9975-10 with new date.
194 :    
195 : maechler 1767 * R/Ops.R (Arith): make sure Csparse o Csparse also works for e.g. ntCMatrix
196 :     * tests/simple.R: test the above and some of these coercions:
197 :    
198 :     * R/nsparseMatrix.R: coercing "Csparse" to "lsparseMatrix";
199 :     be careful to avoid infinite recursion, using new coercions in
200 :     * R/ngCMatrix.R and nsC... and ntC...
201 :     * R/lsparseMatrix.R: ditto
202 :    
203 : maechler 1765 * R/SparseM-conv.R: more conversion, notably for triplet matrices.
204 :    
205 : maechler 1767 * src/dgCMatrix.c (R_to_C_Matrix): port Doug's fix and
206 :     * R/Rsparse.R: reactivate .Call()s
207 : maechler 1765
208 : maechler 1767 * tests/Class+Meth.R: a bit more on actual classes
209 :    
210 :     2007-02-04 Douglas Bates <bates@stat.wisc.edu>
211 :    
212 :     * src/dgCMatrix.c (compressed_to_TMatrix): fix memory bug using strdup()
213 :    
214 : maechler 1760 2007-02-03 Martin Maechler <maechler@stat.math.ethz.ch>
215 : maechler 1758
216 :     * DESCRIPTION (Version): 0.9975-10 to upload
217 :    
218 : maechler 1760 * tests/Class+Meth.R (tstMatrixClass): require coercions to
219 :     specific classes less unconditionally.
220 :    
221 :     * R/Auxiliaries.R: get rid of as_Tsparse() and as_Rsparse()
222 :    
223 :     * R/Tsparse.R (triu): etc, use as(*, "TsparseMatrix") instead of as_Tsparse()
224 :    
225 :     * R/Rsparse.R (.R.2.T): R-level workaround using compressed_to_TMatrix.
226 : maechler 1758 * R/Rsparse.R (.R.2.C): R-level workaround since C-level
227 :     R_to_CMatrix segfaults on one platform.
228 : maechler 1760 Eliminate most coercion method to *specific* classes, and replace
229 :     with virtual classes coercions.
230 : maechler 1758
231 : maechler 1760
232 : maechler 1758 2007-02-01 Martin Maechler <maechler@stat.math.ethz.ch>
233 :    
234 :     * src/init.c: export the CHM...._validate() placeholders, since
235 :     they *are* called.
236 :    
237 : maechler 1760 * tests/Class+Meth.R (classCanCoerce): and starting to test
238 : maechler 1758 all as(<from>, <to>)
239 :    
240 : maechler 1751 2007-01-30 Martin Maechler <maechler@stat.math.ethz.ch>
241 :    
242 :     * R/Tsparse.R ([): more care when subsetting triangular Tsparse
243 :     * tests/indexing.R: tested now
244 :     * tests/indexing.Rout.save: updated
245 :    
246 :     * src/Csparse.c (Csparse_to_dense): use Rkind = -1 for PATTERN to
247 :     * src/chm_common.c (chm_dense_to_SEXP): return "ngeMatrix" when
248 :     appropriate.
249 :    
250 :     * NAMESPACE: export a trivial
251 :     * R/Matrix.R: drop() Matrix-method
252 :    
253 :     * R/AllClass.R: moved all prototypes to virtual super classes.
254 :    
255 :     * R/Rsparse.R: many more coercions to have less exceptions in
256 :     * tests/Class+Meth.R:
257 :    
258 :     * R/Ops.R (Compare): tweak for case with NA
259 :     * tests/simpl.R: hence another 'FIXME' eliminated
260 :    
261 : maechler 1747 2007-01-29 Martin Maechler <maechler@stat.math.ethz.ch>
262 :    
263 : maechler 1748 * R/diagMatrix.R (solve): the obvious methods for diagonalMatrix
264 :     objects.
265 :    
266 : maechler 1747 * tests/Class+Meth.R (tstMatrixClass): now testing diag(), nnzero(),
267 :     and more of "!", "&", "|", all, any; coercions
268 :    
269 :     * R/Rsparse.R: many coercions (which enable quite a few other
270 :     methods), thanks to enhancements in
271 :     * src/dgCMatrix.c (R_to_CMatrix): new, and
272 :     * src/dgCMatrix.c (compressed_to_TMatrix): now for (d,l,n) ,
273 :     symmetric & triangular and ..RMatrix objects.
274 :    
275 :     * src/TMatrix_as.c (Matrix_T_as_DENSE,Matrix_T_as_GENERAL):
276 :     renamed file from src/dsTMatrix.c;
277 :     now dealing with symmetric and triangular Tsparse coercions, both
278 :     to dense and general.
279 :    
280 :     2007-01-27 Martin Maechler <maechler@stat.math.ethz.ch>
281 :    
282 :     * src/dsTMatrix.c: has now "l" and "n" methods besides the "d" ones.
283 :    
284 :     * R/Ops.R (Arith): <dgCMatrix> o <numeric> now remains sparse
285 :     where sensible when the <numeric> is of length > 1.
286 :    
287 :     2007-01-26 Martin Maechler <maechler@stat.math.ethz.ch>
288 :    
289 :     * R/Matrix.R ([<-): for M[] <- value: fix length
290 :    
291 :     2007-01-25 Martin Maechler <maechler@stat.math.ethz.ch>
292 :    
293 :     * R/Auxiliaries.R (n2l_Matrix): new, to be used in
294 :     * R/ndenseMatrix.R: new coercions n* -> l*
295 :    
296 : maechler 1738 2007-01-22 Martin Maechler <maechler@stat.math.ethz.ch>
297 :    
298 :     * R/triangularMatrix.R: new file; simple triu() and tril() methods.
299 :    
300 :     * R/Ops.R ("Logic"): and other "Ops", many updates
301 :    
302 :     2007-01-18 Martin Maechler <maechler@stat.math.ethz.ch>
303 :    
304 :     * src/Mutils.h (SET_DimNames): new utility
305 :    
306 :     * R/Auxiliaries.R (nnzero): improved and now exported via
307 :    
308 :     * NAMESPACE: + nnzero(); length() == prod(dim(.)) method for all "Matrix" objects
309 :    
310 : maechler 1725 2007-01-17 Martin Maechler <maechler@stat.math.ethz.ch>
311 :    
312 :     * R/diagMatrix.R (!): fix typo.
313 :    
314 :     2007-01-16 Martin Maechler <maechler@stat.math.ethz.ch>
315 :    
316 :     * R/Auxiliaries.R (as_Csparse): and quite a few others:
317 :     allow to pass class definition --> speedup
318 :     * R/sparseMatrix.R: apply the above
319 :    
320 :     * R/Csparse.R: coercion Csparse* to dense* now preserves shape properties.
321 :    
322 :     * src/Mutils.h (mMatrix_as_geMatrix): new, based on
323 :     * src/Mutils.c (dup_mMatrix_as_geMatrix): new; generalization of
324 :     old dup_mMatrix_as_dgeMatrix), eliminating a long-standing "FIXME".
325 :    
326 :     * src/dense.c (dense_to_Csparse): use new mMatrix_as_geMatrix()
327 :    
328 :     * R/denseMatrix.R (.dense2C): based on dense_to_Csparse: name it,
329 :     and use it for "sparse*" as well, since it's faster than the
330 :     as_Csparse(.) way.
331 :    
332 :     2007-01-15 Martin Maechler <maechler@stat.math.ethz.ch>
333 :    
334 :     * R/Ops.R ("Logic"): more methods, notably an <lgC> o <lgC> one.
335 :    
336 : maechler 1724 2007-01-12 Martin Maechler <maechler@stat.math.ethz.ch>
337 :    
338 :     * R/Tsparse.R (.TM.repl.i.2col): new internal function to be used
339 :     as method for M[ ij ] <- v
340 :     * R/Csparse.R:: go via Tsparse for "M[ij] <- v"
341 :    
342 :     * R/Ops.R: "Compare" for (C|R)sparse: need pointer slot for all
343 :     FALSE answer
344 :    
345 :     * R/Csparse.R (replCmat): fix the "all non-zero" case with reordering
346 :     * tests/indexing.R: test it, and some of the above
347 :    
348 :     2007-01-05 Martin Maechler <maechler@stat.math.ethz.ch>
349 :    
350 :     * R/Auxiliaries.R (is_duplicatedT): new utility
351 :    
352 : bates 1716 2007-01-05 Douglas Bates <bates@stat.wisc.edu>
353 :    
354 :     * src/init.c (R_init_Matrix): export cholmod_scale
355 :    
356 : maechler 1724 2006-12-30 Martin Maechler <maechler@stat.math.ethz.ch>
357 :    
358 :     * R/zzz.R (tmp): for R >= 2.5.0, extend formals of our
359 :     base::as.matrix to (x, ...)
360 :    
361 : maechler 1714 2006-12-28 Martin Maechler <maechler@stat.math.ethz.ch>
362 :    
363 :     * R/Ops.R ("Arith" etc): move almost all "Ops" methods to new R
364 :     file; start using "Logic", hence
365 :    
366 :     * DESCRIPTION (Depends): R >= 2.4.1 (since we want "Logic")
367 :     * NAMESPACE: import and export "Logic"
368 :    
369 :     2006-12-27 Martin Maechler <maechler@stat.math.ethz.ch>
370 :    
371 :     * src/zpotfr.f and dependencies: use LAPACK 3.1 version
372 :     only needed previously to R version 2.5.0.
373 : maechler 1724
374 : maechler 1710 2006-12-26 Martin Maechler <maechler@stat.math.ethz.ch>
375 :    
376 :     * DESCRIPTION (Date, Version): 0.9975-8, ready for release
377 :    
378 :     * R/Tsparse.R (replTmat): fix subassignment of triangular
379 :     * R/Csparse.R (replCmat): ditto
380 :     * tests/indexing.R: more tests, incl the above fix
381 :    
382 :     2006-12-23 Martin Maechler <maechler@stat.math.ethz.ch>
383 :    
384 :     * R/Auxiliaries.R (drop0): extend for non CSparse
385 :     * R/Auxiliaries.R (diagU2N): should work for all sparseMatrix
386 :    
387 :     * src/Csparse.c (Csparse_to_Tsparse, Csparse_general_to_symmetric):
388 :     use uplo correctly (!); other places: use uplo_P() macro
389 :    
390 :     * R/Csparse.R (replCmat): call diagU2N() when needed
391 :     * R/Tsparse.R (replTmat): ditto
392 :    
393 :     * src/dtCMatrix.c (tCMatrix_validate): new
394 :     * src/dtTMatrix.c (tTMatrix_validate): new, used in
395 :     * R/AllClass.R: for validity of dtC, dsC, and dtT, dsT.
396 :    
397 :     * R/diagMatrix.R (replDiag): to use in [<-
398 :    
399 : maechler 1708 2006-12-22 Martin Maechler <maechler@stat.math.ethz.ch>
400 :    
401 :     * R/Auxiliaries.R (as_Csparse2, as_geSimpl): new functions;
402 :     also more general diagU2N().
403 :    
404 :     2006-12-21 Martin Maechler <maechler@stat.math.ethz.ch>
405 :    
406 :     * R/bind2.R: new file for all cbind2(), rbind() methods moved here
407 :     from R/<foo>Matrix.R files. Better diagonal & improved sparse methods.
408 :    
409 : maechler 1707 2006-12-20 Martin Maechler <maechler@stat.math.ethz.ch>
410 :    
411 :     * tests/bind.R: a few more cases
412 :     * R/Auxiliaries.R (.M.kind): also work for atomic vectors
413 :    
414 :     * R/denseMatrix.R (cbind2/rbind2): moved here (and generalized) from
415 :     * R/ddenseMatrix.R (cbind2/rbind2)
416 :     * R/Tsparse.R (replTmat): final(?!) fix for "[<-" ..
417 :     * tests/indexing.R
418 :     * tests/indexing.Rout.save: updated
419 :    
420 :     2006-12-18 Martin Maechler <maechler@stat.math.ethz.ch>
421 :    
422 :     * R/Tsparse.R (replTmat): fixed a remaining "[<-" bug in
423 :     * tests/indexing.R
424 :    
425 : maechler 1705 2006-12-15 Martin Maechler <maechler@stat.math.ethz.ch>
426 :    
427 :     * R/sparseMatrix.R (prSpMatrix): "." alignment much improved:
428 :     align with proper position of "0", i.e., right for integers.
429 :     argument 'align' by default is "fancy".
430 :    
431 :     2006-12-14 Martin Maechler <maechler@stat.math.ethz.ch>
432 :    
433 :     * R/sparseMatrix.R: delegate "Compare" to "Csparse.."
434 :     * R/Csparse.R: and fix "Compare" for more cases.
435 :     * tests/Class+Meth.R: test some of these (m == m, m != m)
436 :    
437 :     2006-12-13 Martin Maechler <maechler@stat.math.ethz.ch>
438 :    
439 :     * R/lsparseMatrix.R: all() and any() methods
440 :     * R/ldenseMatrix.R: ditto
441 :     * NAMESPACE, R/Matrix.R: ditto
442 :    
443 :     * man/all-methods.Rd: document them minimally
444 :    
445 :     * tests/simple.R: add a few examples for these
446 :    
447 : maechler 1696 2006-12-11 Martin Maechler <maechler@stat.math.ethz.ch>
448 :    
449 :     * R/Tsparse.R ([): fix long standing typo in symmetric case
450 :     * man/dsCMatrix-class.Rd: add example exhibiting the above case
451 :    
452 : bates 1691 2006-12-10 Douglas Bates <bates@stat.wisc.edu>
453 :    
454 :     * src/CHMfactor.c (CHMfactor_to_sparse): change LDL factorization
455 :     to LL before converting to a sparse matrix. (The LDL form can be
456 :     converted to a sparse matrix but it is implicitly a unit
457 :     triangular matrix and a diagonal matrix overwritten on the diagonal.)
458 :    
459 :     2006-12-09 Douglas Bates <bates@stat.wisc.edu>
460 :    
461 :     * src/chm_common.c (chm_factor_to_SEXP): allocate and fill the Dim slot.
462 :    
463 : bates 1688 2006-12-08 Douglas Bates <bates@stat.wisc.edu>
464 :    
465 :     * DESCRIPTION (Version): updated -> release 0.9975-7
466 :     * src/{init.c,chm_common.c}, inst/include/*: export cholmod_analyze_p
467 :    
468 : maechler 1682 2006-11-30 Martin Maechler <maechler@stat.math.ethz.ch>
469 :    
470 :     * R/diagMatrix.R (%*%): write a direct [diag o Csparse] method
471 :    
472 : bates 1681 2006-11-29 Douglas Bates <bates@stat.wisc.edu>
473 :    
474 :     * src/dgeMatrix.c (dgeMatrix_solve): Check error code from dgetri.
475 :     * tests/dg_Matrix.R: Add Barry Rowlingson's test of a matrix that
476 :     is exactly singular.
477 :    
478 : maechler 1674 2006-11-07 Martin Maechler <maechler@stat.math.ethz.ch>
479 :    
480 :     * DESCRIPTION (Date): updated -> release 0.9975-6
481 :    
482 : maechler 1673 2006-11-06 Martin Maechler <maechler@stat.math.ethz.ch>
483 :    
484 :     * R/Csparse.R (replCmat): symmetric indexing of symmetric matrix
485 :     now returns symmetric.
486 :    
487 :     * R/zzz.R ("diag<-"): replace "diag<-" in base for R <= 2.4.x
488 :    
489 :     * R/Matrix.R (.M.sub.i.2col): new, for M[ cbind(i,j) ] indexing.
490 :     * R/Matrix.R (.M.repl.i.2col): new, for M[ cbind(i,j) ] <- value
491 :    
492 :     * R/Auxiliaries.R (.type.kind): added
493 :    
494 :     2006-11-04 Martin Maechler <maechler@stat.math.ethz.ch>
495 :    
496 :     * src/cs.[ch]: updated to CSparse Version 2.0.3 by simply
497 :     running src/CSparse_install.sh
498 :    
499 :     * R/denseMatrix.R: "[": keep symmetric on symmetric indexing.
500 :    
501 : maechler 1665 2006-11-03 Martin Maechler <maechler@stat.math.ethz.ch>
502 :    
503 :     * src/dsCMatrix.c (dsCMatrix_Csparse_solve): new
504 :     * R/dsCMatrix.R (solve): "fully-sparse" using the above.
505 :    
506 :     * R/AllClass.R: "pMatrix" now also inherits from "generalMatrix"
507 :    
508 :     * tests/Class+Meth.R (tstMatrixClass): now assure
509 :     the (important in method programming) property :
510 :    
511 :     ###>> Every "Matrix" is either
512 :     ###>> "general*", "symmetric*", "triangular*" or "diagonal*"
513 :    
514 :     (where "*" stands for "Matrix")
515 :    
516 :     * R/Auxiliaries.R (diagU2N): now .Call()s Csparse_diagU2N for <Csparse>
517 :    
518 :     * R/dMatrix.R (Compare(<dMatrix>,<dMatrix>): update and
519 :     * tests/validObj.R: checks for "comparison"
520 :    
521 :     * R/sparseMatrix.R ([): improved indexing for sparse;
522 :     trying to keep <symmetric>[ n, n] symmmetric
523 :    
524 :     * tests/indexing.R: indexing for logical sparse now ok
525 :    
526 :    
527 : maechler 1660 2006-11-02 Martin Maechler <maechler@stat.math.ethz.ch>
528 :    
529 : maechler 1661 * src/Tsparse.c: use xTsparse_validate() , and hence remove
530 :    
531 :     * src/{ltC,lsC,lgT}Matrix.[ch]: removed
532 :    
533 :     2006-11-02 Martin Maechler <maechler@stat.math.ethz.ch>
534 :    
535 : maechler 1660 * R/AllClass.R (Matrix-class): check length of dimnames in validity.
536 :    
537 :     * tests/simple.R: validObject() checking the above.
538 :    
539 : maechler 1665 * src/dgCMatrix.c (xCMatrix_validate): new, small and simple,
540 : maechler 1660 replacing both dgCMatrix_validate and lgCM*.
541 :    
542 :     * src/Csparse.c (Csparse_dense_prod, etc): do not lose dimnames;
543 :     fix dimnames setting in other places.
544 :     * src/chm_common.c (chm_dense_to_SEXP): now can pass dimnames
545 :    
546 : maechler 1659 2006-11-01 Martin Maechler <maechler@stat.math.ethz.ch>
547 :    
548 : maechler 1660 * R/Csparse.R,src/Csparse.c, etc: tcrossprod(<CsparseM>,<CsparseM>)
549 :    
550 :     * R/sparseMatrix.R (isSymmetric): drop 'factors' slot for
551 :     symmetry test, via
552 : maechler 1659 * R/Auxiliaries.R (.as.dgC.0.factors):
553 :    
554 : bates 1657 2006-11-01 Douglas Bates <bates@r-project.org>
555 :    
556 :     * R/Csparse.R,src/Csparse.c,tests/matprod.R,
557 :     man/CsparseMatrix-class.Rd: crossprod(<CsparseMatrix>,
558 :     <CsparseMatrix>) added
559 :    
560 : maechler 1655 2006-10-30 Martin Maechler <maechler@stat.math.ethz.ch>
561 :    
562 :     * tests/matprod.R: add a variation of Harri's example
563 :    
564 :     * R/dsparseMatrix.R: fix crossprod(<dsparse>, <dge>) to *not*
565 :     recursive infinitely.
566 :    
567 :     * R/dgCMatrix.R: + solve(<sparse>, <sparse>)
568 :    
569 :     * tests/indexing.R: add test for the "<" bug fixed 10-27 in R/dMatrix.R
570 :    
571 :     2006-10-28 Martin Maechler <maechler@stat.math.ethz.ch>
572 :    
573 :     * tests/Class+Meth.R (tstMatrixClass): more: use non-trivial
574 :     matrix if possible; test m+m == 2*m; now test dgRMatrix.
575 :     * R/dgRMatrix.R (.to.dgR): a few more coercions, in order to
576 :     satisfy the above test.
577 :    
578 : maechler 1654 2006-10-27 Martin Maechler <maechler@stat.math.ethz.ch>
579 :    
580 : maechler 1655 * R/Matrix.R (Ops): <Matrix> o <matrix> method added
581 :    
582 : maechler 1654 * R/dgCMatrix.R: solve(a, b="missing") based on
583 :     * src/dgCMatrix.c (dgCMatrix_matrix_solve): extend to work with
584 :     RHS = NULL.
585 :    
586 :     * R/diagMatrix.R (diagdiagprod): extend %*% etc to ldiMatrix;
587 :     add more (needed) [t]crossprod() methods.
588 :    
589 :     * man/ddiMatrix-class.Rd: more info, notably on 'diag'
590 :    
591 :     * R/Auxiliaries.R (as_CspClass): cleanup
592 :     (drop0): internal utility for "Csparse_drop(*, 0)"
593 :     (.bail.out.2): encourage active feedback
594 :    
595 :     2006-10-26 Martin Maechler <maechler@stat.math.ethz.ch>
596 :    
597 :     * R/dMatrix.R(Compare): new(), then slots [no validity check]
598 :    
599 :     * src/Csparse.c (Csparse_validate): fixed (and more efficient in
600 :     non-valid or 'sorted' case).
601 :    
602 :     * R/dsparseMatrix.R: add "chol" method.
603 :     * R/ddenseMatrix.R: ditto
604 :    
605 :     * R/diagMatrix.R (Ops): group methods for <diagonal> o <sparse>
606 :     * NAMESPACE (Ops)
607 :     * R/diagMatrix.R (diag2T): simple utility used "higher level"
608 :     coercion; deprecating direct lower level coercions.
609 :    
610 :     * R/*.R (seq): use seq_len() and seq_along() where possible.
611 :    
612 :    
613 : maechler 1647 2006-10-23 Martin Maechler <maechler@stat.math.ethz.ch>
614 :    
615 :     * DESCRIPTION (Version): 0.9975-5 ready for release
616 :    
617 : bates 1646 2006-10-20 Douglas Bates <bates@stat.wisc.edu>
618 :    
619 :     * src/init.c (R_init_Matrix): export more cholmod CCallable functions.
620 :    
621 : maechler 1642 2006-10-20 Martin Maechler <maechler@stat.math.ethz.ch>
622 :    
623 :     * R/AllClass.R (corMatrix): add 'validity' check;
624 :     comment out unused "LDL" class definition
625 :     * NAMESPACE: mention, but do not export "LDL" class
626 :     * R/corMatrix.R: new (simple), needed for R-devel with
627 :     * tests/Class+Meth.R (tstMatrixClass): 1 exception for corMatrix
628 :     coerce and t() exceptions for all 5 'Mat.MatFact' classes.
629 :    
630 : bates 1641 2006-10-19 Douglas Bates <bates@stat.wisc.edu>
631 :    
632 :     * src/chm_common.h: Add R_cholmod_start to initialize cholmod to
633 :     use Rprintf and R's error handling.
634 :    
635 : maechler 1635 2006-10-17 Martin Maechler <maechler@stat.math.ethz.ch>
636 :    
637 :     * R/diagMatrix.R (%*%): rep(*, each = .) in Matrix %*% diagonal.
638 :     * tests/matprod.R: add tests for the bug fixed.
639 :    
640 : bates 1624 2006-10-11 Douglas Bates <bates@stat.wisc.edu>
641 :    
642 :     * src/HBMM.[ch]: remove HarwellBoeing format for writing.
643 :     * src/SOURCES_C.mkf (SOURCES_C): no longer compile iohb.c
644 :    
645 :     2006-10-06 Douglas Bates <bates@stat.wisc.edu>
646 :    
647 : bates 1629 * R/d[gs]CMatrix.R: deprecate the writeHB function. Use writeMM instead.
648 : bates 1624
649 : maechler 1618 2006-10-06 Martin Maechler <maechler@stat.math.ethz.ch>
650 :    
651 :     * DESCRIPTION (Version): 0.9975-3
652 :    
653 :     * R/diagMatrix.R (bdiag): new function constructing block diagonal
654 :     (sparse) matrices.
655 :     * man/bdiag.Rd: docu + examples
656 :    
657 : maechler 1619 * R/Csparse.R (replCmat): calling new Csparse_drop() now.
658 :    
659 : maechler 1618 * src/Csparse.c (Csparse_general_to_symmetric, Csparse_drop): new functions
660 :     * R/lsCMatrix.R: three more coercions to lsC (thanks to the above)
661 :    
662 :     * R/diagMatrix.R (Diagonal): '[<-' method for diag.matrices such
663 :     that result is sparse or diagonal (and not dense).
664 :    
665 :     * man/Subassign-methods.Rd: fix examples
666 :    
667 :     * R/Matrix.R (Matrix): Matrix(0, *) or Matrix(*, sparse=TRUE)
668 :     should always return a sparse (and not sometimes a diagonal) matrix.
669 :    
670 : maechler 1615 2006-10-05 Martin Maechler <maechler@stat.math.ethz.ch>
671 :    
672 :     * R/Matrix.R ([<-): also for value "Matrix" or "matrix"
673 :    
674 : bates 1613 2006-10-04 Douglas Bates <bates@stat.wisc.edu>
675 :    
676 :     * DESCRIPTION (Version): 0.9975-2
677 : maechler 1615
678 : bates 1613 * inst/include/Matrix_stubs.c (M_cholmod_sparse_to_triplet): export more symbols
679 :    
680 : bates 1611 2006-10-02 Douglas Bates <bates@R-project.org>
681 :    
682 :     * tests/dg_Matrix.R: Simplify test taking into account new code.
683 :    
684 : maechler 1599 2006-09-29 Martin Maechler <maechler@stat.math.ethz.ch>
685 :    
686 : maechler 1600 * R/Csparse.R (replCmat): improve for missing i / j in non-simple cases
687 :    
688 : maechler 1599 * R/lsTMatrix.R: new files w/ missing methods
689 :     * R/nsTMatrix.R: " 'for completeness'
690 :    
691 :     * tests/Class+Meth.R: a bit less 'not.ok.classes'
692 :    
693 :     * R/Tsparse.R (t): generalized "t" method from "dgT*" to "Tsparse*"
694 :    
695 :    
696 : bates 1595 2006-09-28 Douglas Bates <bates@R-project.org>
697 :    
698 :     * src/dppMatrix.h: Ensure definition of dspMatrix_validate is
699 :     included.
700 :    
701 :     * src/init.c, inst/include/{Matrix.h,Matrix_stubs.h,cholmod.h}:
702 :     Export C-callable functions used in Zt_create in lme4.
703 :    
704 : maechler 1592 2006-09-28 Martin Maechler <maechler@stat.math.ethz.ch>
705 :    
706 :     * DESCRIPTION (Version): 0.9975-1
707 :    
708 :     * tests/simple.R: less checks fail; using NA, found that our
709 :     kronecker() is not base-compatible with NA's.
710 :    
711 :     * R/dMatrix.R: "Compare" method now implemented for all cases
712 :    
713 :     * R/Auxiliaries.R (indTri): == which([lower/upper].tri( * )) new utility
714 :    
715 :     * man/dtpMatrix-class.Rd: mention length of 'x' slot
716 :    
717 :     * src/dtpMatrix.c (dtpMatrix_validate): fix check
718 :     * src/dspMatrix.c (dspMatrix_validate): ditto
719 :    
720 :     * R/dtTMatrix.R (gt2tT): fix ("l" -> "n")
721 :     including coercion to [nl]tTMatrix.
722 :    
723 :     * R/diagMatrix.R (show): print a header line as for other classes.
724 :    
725 :     2006-09-27 Martin Maechler <maechler@stat.math.ethz.ch>
726 :    
727 :     * src/Makefile.win (SUBDIRS): fix typo
728 :    
729 : maechler 1583 2006-09-19 Martin Maechler <maechler@stat.math.ethz.ch>
730 :    
731 :     * DESCRIPTION (Date): ready to release 0.9975-0 to CRAN
732 :    
733 : bates 1577 2006-09-18 Douglas Bates <bates@stat.wisc.edu>
734 :    
735 :     * R/[CT]sparse.R (crossprod and tcrossprod): Handle the cases for x
736 :     symmetric and y missing in R code using %*% (cholmod_aat doesn't
737 :     accept a symmetric matrix).
738 :     * tests/group-methods.R: Uncomment test of crossprod applied to
739 :     lsCMatrix objects.
740 :    
741 : maechler 1575 2006-09-18 Martin Maechler <maechler@stat.math.ethz.ch>
742 :    
743 :     * R/AllClass.R (symmetricMatrix): add validity method (available
744 :     in C for a long time). Many "n..Matrix": drop (wrong) validity arg.
745 :    
746 :     * src/lgCMatrix.c (lgCMatrix_validate): check 'x' slot (!)
747 :    
748 :     * tests/indexing.Rout.save:
749 :     * tests/indexing.R: additions, mainly for 'lsparse'
750 :    
751 :     * R/diagMatrix.R (Diagonal) & coercion to lgTMatrix: fixes for NA
752 :     case.
753 :    
754 :     * R/Auxiliaries.R (nz.NA): new utility now used in nnzero()
755 :    
756 : maechler 1571 2006-09-16 Martin Maechler <maechler@stat.math.ethz.ch>
757 :    
758 : maechler 1572 * R/sparseMatrix.R (prSpMatrix): print logical NAs "visibly"
759 :     as 'N' (1-letter - Ok?)
760 :    
761 : maechler 1571 * tests/group-methods.R: add test for logical + NAs
762 :    
763 :     * R/dMatrix.R ("Compare"): fix to work with NA's
764 :    
765 :     * R/AllClass.R: "Cholesky" etc now inherit from MatrixFactorization.
766 :    
767 :     * src/lgCMatrix.c (ncsc_to_matrix): renamed from lcsc_to_matrix()
768 :     which is implemented.
769 :    
770 : maechler 1565 2006-09-15 Martin Maechler <maechler@stat.math.ethz.ch>
771 :    
772 : maechler 1571 * src/chm_common.c: coerce logical <-> double instead of
773 :     typecasting; needed for "l" matrix handling in cholmod.
774 : maechler 1565
775 : maechler 1571 * tests/other-pkgs.R (graph): small extension in "graph" checks.
776 :    
777 : maechler 1565 * R/sparseMatrix.R (graphNEL -> Tsparse): method for weight case.
778 :     (Tsp2grNEL): other fixes needed
779 :    
780 : maechler 1548 2006-09-11 Martin Maechler <maechler@stat.math.ethz.ch>
781 :    
782 :     * R/AllClass.R ("nMatrix"): and subclasses for "nonzero pattern"
783 :     Matrices, since "lMatrix", also "lsparseM" can have NA
784 :     * R/ndenseMatrix.R, etc: new source files
785 :     * man/nsparseMatrix-classes.Rd, etc: new help files
786 :     * tests/: adaptions
787 :     * src/chm_common.c (chm_dense_to_SEXP): and others:
788 :     new 'Rkind' argument: "l*" and "d*" both use CHOLMOD_REAL
789 : maechler 1582 * src/Csparse.c, etc: ditto
790 : maechler 1548
791 : bates 1546 2006-09-11 Douglas Bates <bates@R-project.org>
792 :    
793 :     * src/Mutils.[ch],init.c inst/include/*.h: Move the
794 :     alloc_d**Matrix functions to the lme4 package.
795 :    
796 : bates 1543 2006-09-09 Douglas Bates <bates@R-project.org>
797 :    
798 :     * src/dsCMatrix.c (dsCMatrix_Cholesky): igoring LDL = FALSE now
799 : maechler 1544 fixed
800 : bates 1543
801 : maechler 1544 2006-09-09 Martin Maechler <maechler@stat.math.ethz.ch>
802 :    
803 : maechler 1548 * R/lMatrix.R: new
804 :    
805 : maechler 1544 * R/sparseMatrix.R (Tsp2grNEL): do not yet use graph::foo()
806 :    
807 :     * R/dgeMatrix.R: do not define tcrossprod() methods for "matrix"
808 : maechler 1582 * man/tcrossprod.Rd: ditto
809 : maechler 1544
810 : bates 1538 2006-09-08 Douglas Bates <bates@stat.wisc.edu>
811 :    
812 :     * inst/include/Matrix_stubs.c,Matrix.h: Add declarations and stubs
813 :     for exported functions
814 :     * src/Makefile, src/CHOLMOD/Lib/Makefile, src/Metis,CAMD,CCOLAMD:
815 :     Remove partitioning algorithms for sparse matrix reordering. The
816 :     copyright on the Metis code was problematic and the methods were
817 :     rarely used.
818 :     * src/triplet_to_col.[ch],MMHB.[ch]: Remove triplet_to_col. Such
819 :     operations are now done entirely in CHOLMOD code.
820 :    
821 : bates 1517 2006-09-06 Douglas Bates <bates@R-project.org>
822 :    
823 :     * src/Mutils.h: Remove functions that are no longer used.
824 :    
825 : bates 1507 2006-09-04 Douglas Bates <bates@R-project.org>
826 :    
827 :     * src/dtCMatrix.c (dtCMatrix_validate): rename functions.
828 :     * src/DEPS.mkf: update
829 :    
830 : maechler 1481 2006-09-02 Martin Maechler <maechler@stat.math.ethz.ch>
831 :    
832 :     * created branches/Matrix-for-R-2.3.x; on trunk: do
833 :     * DESCRIPTION (Version): 0.9975-0
834 :     (Depends): R (>= 2.4.0)
835 :    
836 : bates 1475 2006-09-01 Douglas Bates <bates@R-project.org>
837 :    
838 :     * R/sparseMatrix.R: Added direct method to CsparseMatrix from graphNEL
839 :    
840 : maechler 1472 2006-09-01 Martin Maechler <maechler@stat.math.ethz.ch>
841 :    
842 :     * R/sparseMatrix.R: add coercion from "ANY" to "sparseMatrix"
843 :     * R/denseMatrix.R: add coercion from "ANY" to "denseMatrix"
844 :    
845 :     * R/Matrix.R ([): use nargs() to disambiguate M[i] and M[i,]
846 :    
847 :     2006-08-31 Martin Maechler <maechler@stat.math.ethz.ch>
848 :    
849 :     * R/sparseMatrix.R (Arith): moved Arith group method one-level up
850 :     from "dsparse" to "sparse" and now go via "Csparse" instead of "dgC"
851 : maechler 1582 * R/dsparseMatrix.R: ditto
852 :     * R/Csparse.R: ditto
853 : maechler 1472
854 :     2006-08-31 Martin Maechler <maechler@stat.math.ethz.ch>
855 :    
856 :     * R/dMatrix.R (Compare): improve availability of "<", etc
857 :     * R/Auxiliaries.R (asTuniq): new; also make use of R 2.4.x print(*,max)
858 :    
859 : maechler 1467 2006-08-30 Martin Maechler <maechler@stat.math.ethz.ch>
860 :    
861 :     * R/dgCMatrix.R: aargh: "Arith(<dgC>, numeric)" was wrong because
862 :     of a 0-index which was used as 1-index (..hmm)
863 :    
864 :     * R/sparseMatrix.R (prSpMatrix): fix printing an all-0 sparse Matrix
865 :    
866 :     * R/Auxiliaries.R (all0, is0): for 0-testing in presence of NA's
867 :     * R/Auxiliaries.R (isTriMat): use all0() for 0-testing.
868 : maechler 1582 (.is.diagonal): ditto
869 : maechler 1467
870 :     * R/lgTMatrix.R: as("matrix", "lgTMatrix"): warn about NA's
871 :    
872 :     * R/Matrix.R (Matrix): also work for NA data
873 :    
874 : maechler 1455 2006-08-28 Martin Maechler <maechler@stat.math.ethz.ch>
875 :    
876 :     * R/Matrix.R (Matrix): + 'forceCheck' argument; dimnames setting
877 :     in all cases.
878 :    
879 : bates 1453 2006-08-27 Douglas Bates <bates@R-project.org>
880 :    
881 :     * src/dense.[ch],init.c, R/ddenseMatrix.R, man/band.Rd
882 :     (ddense_band): Added triu, tril and band for ddenseMatrix objects.
883 :    
884 : maechler 1447 2006-08-25 Martin Maechler <maechler@stat.math.ethz.ch>
885 :    
886 :     * src/Mutils.c (dup_mMatrix_as_dgeMatrix): added all subclasses of
887 :     subclasses of "ddenseMatrix"
888 :     * src/init.c et al: outcomment dtrM*_as_dge* and dsyM*_as_dge*_
889 :     * R/ddenseMatrix.R et al: setAs("ddenseMatrix", "dgeMatrix", ..)
890 :     instead of half dozen specialized ones.
891 :    
892 : bates 1445 2006-08-25 Douglas Bates <bates@R-project.org>
893 :    
894 :     * R/lmer.R (qqmath method): Bug fix provided by Emmanuel Tillard
895 :     <tillard@cirad.fr> - ordering standard errors to match effects.
896 :    
897 : bates 1439 2006-08-24 Douglas Bates <bates@R-project.org>
898 : bates 1431
899 : bates 1439 * src/lsCMatrix.c (lsCMatrix_trans): Remove lsCMatrix_chol based
900 :     on R_ldl.
901 :     * R/lCholCMatrix.R,
902 :     src/[dl]CholCMatrix.[ch],R_ldl.[ch],Metis_utils.[ch]: removed
903 :     * src/dsCMatrix.c (dsCMatrix_to_dgTMatrix): use CHOLMOD
904 :     * many files in ./R and ./src: Use more general version of
905 :     dup_mMatrix_as_dgeMatrix to simplify method definitions.
906 : bates 1442 * src/Mutils.c (dup_mMatrix_as_dgeMatrix): Add ddiMatrix,
907 :     dtpMatrix, dspMatrix and dppMatrix conversions.
908 :    
909 : maechler 1447
910 : bates 1439 2006-08-23 Douglas Bates <bates@R-project.org>
911 :    
912 :     * R/AllClass.R,lCholCMatrix.R,src/SOURCES_C.mkf,init.c,NAMESPACE:
913 :     Remove classes lCholCMatrix and dCholCMatrix based on R_ldl code.
914 : bates 1431 * src/dgeMatrix.c: Ensure 'factors' slot exists in result of
915 :     dgeMatrix_crossprod (may need to do this in other places).
916 :     * R/AllGeneric.R,dsCMatrix.R, src/dscMatrix.[ch]: Add Cholesky
917 :     generic and method for dsCMatrix. Use CHOLMOD for chol().
918 :    
919 : bates 1414 2006-08-22 Douglas Bates <bates@R-project.org>
920 :    
921 :     * src/Mutils.c (dup_mMatrix_as_dgeMatrix): updated for general
922 :     types of classed Matrices, matrices or numeric or logical vectors.
923 : bates 1423 * src/init.c: register dup_mMatrix_as_dgeMatrix for coercions.
924 :     * src/chm_common.c,Mutils.h (as_cholmod_factor): Move check_class
925 :     to Mutils.h (as an inline) and change name to Matrix_check_class;
926 :     fixes in as_cholmod_factor and chm_factor_to_SEXP.
927 :     * src/dsCMatrix.[ch]: Use CHOLMOD for dsCMatrix_chol and
928 :     dsCMatrix_matrix_solve. Comment out vestigial functions.
929 :     * src/Csparse.c: use diag_P and uplo_P macros.
930 : maechler 1447
931 : bates 1405 2006-08-21 Douglas Bates <bates@R-project.org>
932 :    
933 :     * src/lmer.c (internal_mer_RZXinv): Fix memory leak caught by
934 : maechler 1447 valgrind.
935 : bates 1411 * tests/matprod.R: Add tests to verify that 'solve' and '%*%' are
936 :     inverses.
937 :     * src/sparseQR.c (sparseQR_validate): add new validation test, fix
938 :     -Wall warnings.
939 :     * src/dppMatrix.c,dtrMatrix.c,dgCMatrix.c,dgeMatrix.c,dspMatrix.c:
940 :     Use dup_mMatrix_as_dgeMatrix.
941 : maechler 1447
942 : bates 1403 2006-08-20 Douglas Bates <bates@R-project.org>
943 :    
944 :     * src/sparseQR.c: Fix thinko in sparseQR_resid_fitted.
945 :     * tests/sparseQR.R: Added
946 :     * man/sparseQR-class.Rd: Document methods for qr.* generics
947 :     * R/sparseQR.R: Return correct # of coefs; fix cut-and-paste errors
948 :    
949 : bates 1398 2006-08-19 Douglas Bates <bates@R-project.org>
950 :    
951 :     * NAMESPACE, R/sparseQR.R, src/init.c,sparseQR.[ch],SOURCES_C.mkf:
952 :     Added methods for sparseQR for qr.qy, qr.qty, qr.coef, qr.resid
953 :     and qr.fitted.
954 :     * src/Mutils.[ch]: Added dup_mMatrix_as_dgeMatrix utility
955 :     * src/dgCMatrix.c: Check for ordering before storing q in dgCMatrix_QR
956 :    
957 : maechler 1389 2006-08-18 Martin Maechler <maechler@stat.math.ethz.ch>
958 :    
959 :     * R/AllGeneric.R: add "qr" and "chol" generics; via 'trick' since
960 :     the base version has no "..." argument.
961 :    
962 :     * R/sparseMatrix.R (prSpMatrix): fix the triangular unit diagonal case.
963 :    
964 :     * R/Matrix.R: define and
965 :     * NAMESPACE: export as.numeric() and as.logical() methods.
966 :     Let's hope these do not badly slow down something...
967 :     Finally export the zapsmall() method.
968 :    
969 : bates 1388 2006-08-17 Douglas Bates <bates@R-project.org>
970 :    
971 :     * src/dgCMatrix.[ch] (dgCMatrix_matrix_solve), src/init.c,
972 :     R/dgCMatrix.R: solve methods for dgCMatrix and dense RHS.
973 :     * src/dtCMatrix.c :Remove code that is no longer used
974 :     * R/dtCMatrix.R: Use C code for diagU2N in CsparseMatrix classes
975 :    
976 : bates 1370 2006-08-14 Douglas Bates <bates@R-project.org>
977 :    
978 : bates 1373 * src/Csparse.[ch],init.c (Csparse_to_logical): Added utilities
979 :     Csparse_to_logical and Csparse_symmetric_to_general.
980 :     * R/dgCMatrix.R,dsCMatrix.R,Csparse.R : Consolidate general
981 : maechler 1389 coercion methods between CsparseMatrix and TsparseMatrix.
982 : bates 1373
983 :     2006-08-14 Douglas Bates <bates@R-project.org>
984 :    
985 : bates 1370 * R/dtCMatrix.R,dgCMatrix.R,Csparse.R src/init.c,dgCMatrix.[ch],
986 :     Csparse.[ch],chm_common.c,dense.c : Use CHOLMOD code and methods
987 :     for CsparseMatrix, TsparseMatrix, denseMatrix or matrix when
988 :     possible.
989 :    
990 : bates 1368 2006-08-12 Douglas Bates <bates@R-project.org>
991 :    
992 :     * src/chm_common.[ch],Csparse.[ch],Tsparse.[ch],CHMfactor.c,dtTMatrix.c,
993 :     dgTMatrix.c,dgCMatrix.c,dsCMatrix.c,dtTMatrix.c, R/dsTMatrix.R,
994 :     Tsparse.R,Csparse.R,dgTMatrix.R,dsCMatrix.R,lsCMatrix.R:
995 :     generalize conversions between TsparseMatrix, CsparseMatrix,
996 :     denseMatrix and matrix. Preserve triangularity property and
997 :     propagate Dimnames in the easy cases.
998 :    
999 : bates 1365 2006-08-10 Douglas Bates <bates@R-project.org>
1000 :    
1001 :     * src/lmer.c: adjust checks in glmer_init for S4SXP
1002 :     * tests/validObj.R: check of all(eq) should be all(eq@x) - worked
1003 :     before S4SXP but for the wrong reasons.
1004 :    
1005 : bates 1354 2006-08-08 Douglas Bates <bates@R-project.org>
1006 :    
1007 : bates 1360 * src/Csparse.c (Csparse_crossprod): tcrossprod result has stype = -1.
1008 :     Later modified to return the upper triangle only.
1009 :     * R/dgTMatrix.R: Remove vestigial crossprod and tcrossprod methods.
1010 : maechler 1389
1011 : bates 1352 2006-08-07 Douglas Bates <bates@R-project.org>
1012 :    
1013 :     * src/Csparse.c (Csparse_crossprod): Set stype on result to avoid
1014 :     R-level conversion to a sparse symmetric class.
1015 :     * R/Tsparse.R,R/Csparse.R (crossprod and tcrossprod methods):
1016 :     Remove conversion to sparse symmetric classes (now done in C code).
1017 :    
1018 : maechler 1349 2006-08-07 Martin Maechler <maechler@stat.math.ethz.ch>
1019 :    
1020 : maechler 1351 * R/dgCMatrix.R: disable old crossprod and tcrossprod methods
1021 :     * man/band.Rd: adapt the \dontshow{} unit test.
1022 :    
1023 :     2006-08-07 Martin Maechler <maechler@stat.math.ethz.ch>
1024 :    
1025 : maechler 1349 * DESCRIPTION (Version): 0.995-14 for CRAN
1026 :    
1027 :     * tests/other-pkgs.R: oops: library(Matrix) outside *if* !
1028 :    
1029 :     * R/sparseMatrix.R (Tsp2grNEL): fixed Tsparse -> graph coercion
1030 :     * tests/other-pkgs.R: more checks, sparseMatrix -> graph
1031 :    
1032 :     * R/Auxiliaries.R (as_Tsparse, as_Rsparse): new
1033 :     * R/Tsparse.R (tril, triu, band): methods
1034 : bates 1352 * R/dgRMatrix.R (tril, ...): ditto
1035 :     * man/band.Rd: ditto
1036 : maechler 1349
1037 :     2006-08-04 Martin Maechler <maechler@stat.math.ethz.ch>
1038 :    
1039 :     * R/Matrix.R (head, tail): directly use utils:::head.matrix
1040 :     to be up-to-date automatically.
1041 :    
1042 : maechler 1346 2006-08-03 Martin Maechler <maechler@stat.math.ethz.ch>
1043 :    
1044 :     * DESCRIPTION (Version): 0.995-13 to be released to CRAN
1045 :    
1046 :     * DESCRIPTION (Lazydata): no, instead of 'yes' because it fails for:
1047 :     * data/CAex.R, inst/external/CAex_slots.rda: replacing data/CAex.rda
1048 :     * data/KNex.R, inst/external/KNex_slots.rda: replacing data/KNex.rda
1049 :     such that the S4 objects are always created by the current version
1050 :     of R and 'Matrix' class definitions.
1051 :    
1052 : bates 1342 2006-08-01 Douglas Bates <bates@R-project.org>
1053 :    
1054 :     * R/lmer.R (LMEoptimize method), tests/lmer.R,
1055 : maechler 1346 inst/external/test3comp.rda: Added warnings for convergence on
1056 : bates 1342 boundary and test cases.
1057 :    
1058 :     * src/lmer.c (mer_postVar): Modified to return the variances that
1059 :     are marginal to the fixed effects, not conditional on them (which
1060 :     is what the bVar slot contents represent).
1061 :    
1062 : bates 1338 2006-07-31 Douglas Bates <bates@R-project.org>
1063 :    
1064 :     * NAMESPACE, src/lmer.c, R/lmer.R (hatTrace): Add the hatTrace
1065 :     function which calls the C function mer_hat_trace2.
1066 : maechler 1346
1067 : bates 1342 * man/ranef.Rd: Include description of "postVar" argument and
1068 :     producing a caterpillar plot.
1069 : bates 1338
1070 : maechler 1335 2006-07-31 Martin Maechler <maechler@stat.math.ethz.ch>
1071 :    
1072 :     * NAMESPACE: change "correlation" to "corMatrix"
1073 :     * R/AllClass.R: to avoid clash with S3 class in 'nlme'.
1074 : bates 1352 * R/dpoMatrix.R: ditto
1075 :     * R/lmer.R: ditto
1076 : maechler 1335
1077 : bates 1338 2006-07-28 Douglas Bates <bates@R-project.org>
1078 :    
1079 :     * src/lmer.c (internal_mer_RZXinv): Split the calculation of the
1080 :     RZXinv slot's contents into a separate internal function that can
1081 :     be used in mer_hat_trace.
1082 :    
1083 : maechler 1331 2006-07-22 Martin Maechler <maechler@stat.math.ethz.ch>
1084 :    
1085 :     * R/Matrix.R: Coercions "Matrix" -> (sparse|dense)Matrix
1086 :     via new smart
1087 :     * R/Auxiliaries.R (as_Csparse, as_dense, .M.shapse): new
1088 :     utility functions.
1089 :    
1090 :    
1091 : maechler 1330 2006-07-21 Martin Maechler <maechler@stat.math.ethz.ch>
1092 :    
1093 : maechler 1331 * R/Csparse.R (tril, triu, band): do return *triangular* classed
1094 :     matrices when appropriate; band() even symmetric ones.
1095 :     (replCmat): extend to potentially all "CsparseMatrix"
1096 :     * R/Tsparse.R (replTmat): extend to all "TsparseMatrix"; hence
1097 :     allow subassignment for special sparse matrices.
1098 :    
1099 :     * R/Auxiliaries.R (as_geClass): factor out the .M.kind() functionality
1100 :    
1101 : maechler 1330 * src/lmer.c (mer_MCMCsamp, glmer_MCMCsamp): new 'verbose'
1102 :     argument; in glmer_*(): print only if(verbose).
1103 :    
1104 :     speed-optimize a few places by moving REAL(.) out of loops.
1105 :    
1106 :     * src/lmer.h, src/init.h, R/lmer.R: related to above.
1107 :    
1108 : maechler 1329 2006-07-20 Martin Maechler <maechler@stat.math.ethz.ch>
1109 :    
1110 :     * R/Matrix.R("["): disable ("Matrix", i = "logical", j = "missing"),
1111 :     since that wrongly triggers also for M[ logi , ]
1112 :    
1113 :     * R/denseMatrix.R: "[" methods now also work e.g. when indexing
1114 :     a symmetric matrix that results in a non-symmetric one.
1115 :     * R/Auxiliaries.R (as_geClass): new function used in "[" above.
1116 :    
1117 :     * R/dMatrix.R: make round(M) work as round(M, 0)
1118 :    
1119 :     * R/dgTMatrix.R (image): coordinate system and axis now use
1120 :     1-based indices, not 0-based ones.
1121 :    
1122 :     * R/Tsparse.R (.ind.prep for "["): get rid of max(<empty>) warning.
1123 :     * tests/indexing.R: test it.
1124 :    
1125 :     * NAMESPACE: export isSymmetric(); has been a generic in "base" for a while;
1126 :     * man/isSymmetric-methods.Rd: and document it.
1127 :    
1128 :     * R/SparseM-conv.R: added coercion methods for some 'SparseM' matrices.
1129 :     * man/SparseM-conv.Rd: docu them
1130 :    
1131 :     * tests/other-pkgs.R: renamed from tests/graph.R and add example
1132 :     for 'SparseM' conversions
1133 :    
1134 :     2006-07-17 Douglas Bates <Douglas.Bates@R-project.org>
1135 :    
1136 :     * R/Matrix.R (head): added head() and tail() methods.
1137 :    
1138 :     2006-07-17 Martin Maechler <maechler@stat.math.ethz.ch>
1139 :    
1140 :     * DESCRIPTION (Version): 0.995-12 released to CRAN
1141 :    
1142 : maechler 1319 2006-07-15 Martin Maechler <maechler@stat.math.ethz.ch>
1143 :    
1144 :     * tests/simple.R: add check for correct dsT -> dgT coercion;
1145 :     add check for correct printing of symmetric sparse matrices.
1146 :    
1147 :     * R/Auxiliaries.R (non0ind): return *all* non-0 entry indices also
1148 :     for sparse symmetric matrices.
1149 :    
1150 :     * src/dsTMatrix.c (dsTMatrix_as_dgTMatrix): do not copy the
1151 :     diagonal twice.
1152 :    
1153 : bates 1316 2006-07-11 Douglas Bates <Douglas.Bates@R-project.org>
1154 :    
1155 :     * src/dsTMatrix.c (dsTMatrix_as_dgTMatrix): Fix a case of INTEGER
1156 : maechler 1319 being applied to the x slot (detected by Brian Ripley).
1157 : bates 1316
1158 : maechler 1315 2006-07-10 Martin Maechler <maechler@stat.math.ethz.ch>
1159 :    
1160 :     * src/dgCMatrix.c (dgCMatrix_validate): 'p' slot must have correct length.
1161 :    
1162 :     * R/Auxiliaries.R (isTriC): fix buglet (we were 1-based!)
1163 :    
1164 :     2006-07-08 Martin Maechler <maechler@stat.math.ethz.ch>
1165 :    
1166 :     * src/lgCMatrix.c (lgCMatrix_diag): new function
1167 :     * R/lgCMatrix.R (diag): for new method
1168 :    
1169 :     * R/AllClass.R (TsparseMatrix): do use Tsparse_validate
1170 :     ==> construction of illegal "*gTMatrix" via new() should
1171 :     now be much less easy:
1172 :     * tests/Class+Meth.R: assertError() for some illegal "dgT*"
1173 :    
1174 :     * R/Matrix.R (Matrix): Matrix(0, nrow,ncol) now "goes sparse"
1175 :     directly.
1176 :     * man/Matrix.Rd: documents it.
1177 :    
1178 : bates 1311 2006-07-06 Douglas Bates <bates@R-project.org>
1179 :    
1180 :     * src/pedigree.c (pedigree_inbreeding): Correction in
1181 :     initialization. This function is not currently being used and is
1182 :     not fully tested.
1183 :    
1184 : bates 1312 * NAMESPACE, R/{AllClass.R,lmer.R}, src/{init.c,lmer.c}:
1185 :     Introduced the glmer class. Added code for mcmcmsamp on glmer
1186 :     objects. Modified validity check on pedigree objects to account
1187 :     for nonparallel patterns of missingness of parents.
1188 : bates 1311
1189 : bates 1313 * man/{lmer-class.Rd,mcmcsamp.Rd}: Update documentation for glmer
1190 :     class.
1191 : maechler 1315
1192 :     2006-07-01 Martin Maechler <maechler@stat.math.ethz.ch>
1193 :    
1194 :     * R/pMatrix.R: coercion pMatrix -> Tsparse
1195 :    
1196 : bates 1300 2006-06-12 Douglas Bates <bates@R-project.org>
1197 :    
1198 : maechler 1319 * DESCRIPTION (Version): 0.995-11 released to CRAN
1199 :    
1200 : bates 1300 * R/lmer.R (mcmcsamp method): Corrected arrangments of names on
1201 :     the output from mcmcsamp.
1202 :    
1203 : bates 1298 2006-06-10 Douglas Bates <bates@R-project.org>
1204 :    
1205 : bates 1300 * R/lmer.R (simulestimate): added C code for calculating the trace
1206 :     of the hat matrix.
1207 : bates 1298
1208 : maechler 1295 2006-06-09 Martin Maechler <maechler@stat.math.ethz.ch>
1209 :    
1210 :     * R/diagMatrix.R (setAs): define coercion methods to sparse matrix
1211 :     classes.
1212 : maechler 1315 * R/sparseMatrix.R etc: multiplication of diagonal and sparse
1213 : maechler 1295
1214 : maechler 1290 2006-06-08 Martin Maechler <maechler@stat.math.ethz.ch>
1215 :    
1216 :     * R/dgTMatrix.R (colSums): etc. All four of
1217 :     colSums(), rowSums(), colMeans(), rowMeans() now should work for
1218 :     all "Matrices".
1219 :    
1220 : bates 1288 2006-06-01 Douglas Bates <bates@stat.wisc.edu>
1221 :    
1222 :     * R/lmer.R (panel.ci): Add a reference line at zero and a
1223 :     background grid to the qqmath plot of ranef.lmer.
1224 :    
1225 : bates 1287 2006-05-30 Douglas Bates <bates@stat.wisc.edu>
1226 : bates 1284
1227 : bates 1287 * R/lmer.R (expandSlash): Functions (non-exported) to allow nested
1228 :     grouping factors to be specified in the formula as (1|foo/bar).
1229 :    
1230 :     2006-05-27 Douglas Bates <bates@stat.wisc.edu>
1231 :    
1232 : bates 1284 * R/lmer.R (findbars and others): Change check of is.numeric to
1233 :     !is.language to resolve the bug reported by Jacob Wegelin.
1234 :    
1235 :     * src/pedigree.c (pedigree_inbreeding): Initial implementation of
1236 :     code to evaluate inbreeding coefficients without calculating T,
1237 :     based on code in Sargolzaei and Iwaisaki's paper.
1238 :    
1239 : bates 1283 2006-05-27 Douglas Bates <bates@stat.wisc.edu>
1240 :    
1241 :     * R/{lmer.R,AllGeneric.R}, src/{init.c,lmer.[ch]}: Added local
1242 :     generic and mer methods for isNested and denomDF. This denomDF was
1243 :     an attempt to emulate that in lme but I don't think that makes
1244 :     sense. Use the trace of the hat matrix instead.
1245 :    
1246 : maechler 1271 2006-05-17 Martin Maechler <maechler@stat.math.ethz.ch>
1247 :    
1248 :     * R/sparseMatrix.R: Matrix <-> graph methods: can no longer use
1249 :     the C code depending on a slot structure that's no longer valid.
1250 : bates 1352 * src/dgTMatrix.c: ditto (also: src/init.c src/dgTMatrix.h)
1251 : maechler 1271
1252 :    
1253 : bates 1268 2006-05-17 Douglas Bates <bates@stat.wisc.edu>
1254 :    
1255 :     * R/{AllGeneric.R,Csparse.R},man/band.Rd,NAMESPACE: changed name
1256 :     of lowerTriMatrix generic and methods to tril (also upper to triu)
1257 :     and added a general band extractor.
1258 :    
1259 : bates 1267 2006-05-16 Douglas Bates <bates@stat.wisc.edu>
1260 :    
1261 :     * R/pedigree.R (pedigree): Replace sire and dam values outside the
1262 :     allowable range with NAs. Added a corresponding check in the
1263 :     validity check for the pedigree class.
1264 :    
1265 :     * R/[CT]sparse.R ([t]crossprod): The result of single-argument
1266 :     crossprod methods now inherits from symmetricMatrix.
1267 :    
1268 : bates 1265 2006-05-15 Douglas Bates <bates@stat.wisc.edu>
1269 :    
1270 :     * R/AllGeneric.R (lowerTriMatrix): Added (but did not export)
1271 :     generics lowerTriMatrix and upperTriMatrix along with methods for
1272 :     the Csparse virtual class. Also added a C function Csparse_band
1273 :     that implements these methods by calling cholmod_band.
1274 :    
1275 : maechler 1264 2006-05-15 Martin Maechler <maechler@stat.math.ethz.ch>
1276 :    
1277 :     * R/Tsparse.R ("["): column or row subsetting; @Dimnames[k] got
1278 :     erased when it was NULL. This led to invalid subselections!
1279 :    
1280 : bates 1259 2006-04-25 Douglas Bates <bates@stat.wisc.edu>
1281 :    
1282 :     * R/dtCMatrix.R: avoid coercion of dtCMatrix object to dgCMatrix
1283 :     in method for "t" so as not to lose the unit diagonal property.
1284 :    
1285 : bates 1257 2006-04-19 Douglas Bates <bates@stat.wisc.edu>
1286 :    
1287 :     * R/lmer.R, R/AllGeneric.R, NAMESPACE: Remove the postVar generic
1288 :     and methods. This is now an option to the ranef method for the
1289 :     mer class.
1290 :    
1291 :     * src/cs_utils.c: Ensure that the nz component is -1 for a
1292 :     compressed column-oriented matrix. Minor formatting cleanup.
1293 :    
1294 :     * man/lmer-class.Rd: Document the qqmath method for ranef.lmer
1295 :     objects.
1296 :    
1297 : maechler 1253 2006-04-19 Martin Maechler <maechler@stat.math.ethz.ch>
1298 :    
1299 :     * R/Auxiliaries.R (diagU2N): new for the solve() methods in
1300 :     * R/dtCMatrix.R: where dgC -> dgT coercion now preserves diag = "U".
1301 :    
1302 : bates 1251 2006-04-15 Douglas Bates <bates@stat.wisc.edu>
1303 :    
1304 :     * src/cs.[ch],src/cs_utils.[ch] : Added Tim Davis' CSparse library
1305 :     in cs.[ch] and utilities to interface to that code in cs_utils.[ch].
1306 :    
1307 :     * R/dtCMatrix.R, src/dtCMatrix.[ch] : CSparse-based solve methods
1308 :     for the dtCMatrix class.
1309 : maechler 1253
1310 : bates 1247 2006-04-12 Douglas Bates <bates@stat.wisc.edu>
1311 :    
1312 :     * R/pedigree.R, R/AllClass.R, NAMESPACE: added a pedigree class
1313 :     and methods for it.
1314 :    
1315 : maechler 1245 2006-04-12 Martin Maechler <maechler@stat.math.ethz.ch>
1316 :    
1317 :     * R/dgCMatrix.R: add storage.mode(.) <- "double" for "matrix"
1318 :     arguments, such that M %*% 1:6 now works
1319 :     * Tests/matprod.R: test the above
1320 :    
1321 : bates 1244 2006-04-03 Douglas Bates <bates@stat.wisc.edu>
1322 : bates 1243
1323 :     * R/lmer.R (qqmath,ranef.lmer-method): added a qqmath method for
1324 :     the ranef.lmer class.
1325 :    
1326 :     * R/AllClass.R, NAMESPACE, R/lmer.R: Added a postVar generic and
1327 :     methods to extract the posterior variances from the bVar slot.
1328 :    
1329 : maechler 1238 2006-03-30 Martin Maechler <maechler@stat.math.ethz.ch>
1330 :    
1331 :     * R/dtCMatrix.R: allow coercion from dgC* to triangular (dtC*)
1332 :     * R/dsCMatrix.R: and symmetric (dsC*) 'Csparse' matrices.
1333 :    
1334 :     * R/Tsparse.R: Tsparse* -> Csparse* coercion now works and is tested in
1335 :     * tests/simple: (extended)
1336 :    
1337 :     * R/sparseMatrix.R (isTriangular): now using much improved
1338 :     * R/Auxiliaries.R (isTriC): new triangularity check for *CMatrix
1339 :    
1340 : bates 1236 2006-03-23 Douglas Bates <bates@stat.wisc.edu>
1341 :    
1342 :     * src/dsyMatrix.c (dsyMatrix_as_dspMatrix): Propagate DimNames
1343 :     (problem report from Franklin Parlamis). This should be done
1344 : maechler 1238 generally.
1345 : bates 1236
1346 : bates 1234 2006-03-21 Douglas Bates <bates@stat.wisc.edu>
1347 :    
1348 :     * R/AllClass.R,lmer.R: Change the name of the lmer.ranef class to
1349 :     ranef.lmer (like summary.lmer). Add the coef.lmer class and
1350 :     update the plot methods.
1351 :    
1352 : bates 1232 2006-03-20 Douglas Bates <bates@stat.wisc.edu>
1353 :    
1354 :     * R/lmer.R (resid and ranef methods): Added methods for the
1355 :     "residuals" and "resid" generic but only for linear mixed model
1356 :     fits. Changed the ranef method to return a list of data frames so
1357 :     that the plot methods now work.
1358 :    
1359 : bates 1230 2006-03-16 Douglas Bates <bates@bates2>
1360 :    
1361 :     * src/dpoMatrix.c (dpoMatrix_chol): Require n > 0 in call to
1362 :     dpotrf - otherwise the BLAS on Mac OS X complains and quits.
1363 :    
1364 :     * DESCRIPTION (Date): New release
1365 :    
1366 : maechler 1228 2006-03-15 Martin Maechler <maechler@stat.math.ethz.ch>
1367 :    
1368 :     * DESCRIPTION (Version): 0.995-6 -- to be released to CRAN
1369 :    
1370 :     * data/KNex.rda: replacing 'mm' and 'y' by KNex <- list(mm=mm, y=y)
1371 :     * man/KNex.Rd: and other help files
1372 :     * tests/*.R: several ones needed adaption
1373 : bates 1352 * inst/doc/Comparisons.Rnw: ditto
1374 : maechler 1228
1375 : maechler 1226 2006-03-11 Martin Maechler <maechler@stat.math.ethz.ch>
1376 :    
1377 :     * R/dgCMatrix.R (replCmat): "[<-" methods for dgCMatrix
1378 :    
1379 :     * tests/indexing.R: tests for new [<- methods for sparse matrices.
1380 :    
1381 :     2006-03-10 Martin Maechler <maechler@stat.math.ethz.ch>
1382 :    
1383 :     * R/dgTMatrix.R (replTmat): "[<-" methods for dgTMatrix
1384 :    
1385 :     * R/Tsparse.R (.ind.prep): fix out-of-range indexing
1386 :    
1387 :     2006-03-08 Martin Maechler <maechler@stat.math.ethz.ch>
1388 :    
1389 :     * R/dMatrix.R: enable things like M [ M < 10 ]
1390 :     * R/dgeMatrix.R: implement it
1391 :    
1392 : maechler 1222 2006-03-06 Martin Maechler <maechler@stat.math.ethz.ch>
1393 :    
1394 :     * R/AllClass.R: define "summary.mer" and "*.lmer"
1395 :     * R/lmer.R (summary): summary(<mer>) computes & returns the above;
1396 :     * R/lmer.R (show): now works with summary()
1397 :    
1398 :     2006-03-04 Martin Maechler <maechler@stat.math.ethz.ch>
1399 :    
1400 :     * R/dgCMatrix.R: finally direct "Arith" dgC o dgC
1401 :     * R/Auxiliaries.R (WhichintersectInd): and other utilities to
1402 :     support the above
1403 :    
1404 : bates 1213 2006-02-07 Douglas Bates <bates@stat.wisc.edu>
1405 :    
1406 :     * R/lmer.R (lmer): fix initial values of offset and weights for glm.fit.
1407 :     Use glmFit$prior.weights for weights in a glmm.
1408 :     Allow an option usePQL = FALSE to skip the PQL steps for the
1409 :     Laplace method (and, in time, the AGQ method).
1410 :    
1411 :     * src/lmer.c (mer_factor): Move downdating and factoring of XtX
1412 :     into a separate function internal_mer_Xfactor to be able to call
1413 :     it from internal_bhat.
1414 :    
1415 : maechler 1200 2006-01-23 Martin Maechler <maechler@stat.math.ethz.ch>
1416 :    
1417 :     * tests/Class+Meth.R (tstMatrixClass): function for much better
1418 :     testing; now again of all actual classes.
1419 :    
1420 :     * src/Mutils.c (MAKE_TRIANGULAR_BODY, MAKE_SYMMETRIC_BODY):
1421 :     use macros and define make_d_matrix_* and make_i_matrix_*
1422 :     where _i_ is for the ldense routines:
1423 :    
1424 :     * src/ldense.c (ltrMatrix_as_lgeMatrix): provide functions
1425 :     * src/ldense.c (lsyMatrix_as_lgeMatrix):
1426 :    
1427 :     * R/ldenseMatrix.R: use the above in setAs(*,"lgeMatrix")
1428 :    
1429 :    
1430 : maechler 1174 2006-01-16 Martin Maechler <maechler@stat.math.ethz.ch>
1431 :    
1432 :     * R/Matrix.R (Matrix): has become much "smarter" now auto-producing
1433 :     many different kinds of matrices.
1434 :     * R/*.R: quite a few new methods were needed for R CMD check with
1435 :     new Matrix(). Very good for users playing around.
1436 :    
1437 :    
1438 : maechler 1165 2006-01-15 Martin Maechler <maechler@stat.math.ethz.ch>
1439 :    
1440 :     * src/dgeMatrix.c (dMatrix_validate): new
1441 :     * src/Mutils.c (dense_nonpacked_validate): new
1442 :    
1443 :     * src/dtrMatrix.c (dtrMatrix_validate): improved/fixed
1444 :    
1445 :    
1446 :     2006-01-14 Douglas Bates <bates@stat.wisc.edu>
1447 :    
1448 :     * R/AllClass.R (compMatrix), (generalMatrix): new virtual classes
1449 :    
1450 : bates 1123 2006-01-07 Douglas Bates <bates@stat.wisc.edu>
1451 : bates 1119
1452 : maechler 1127 * DESCRIPTION (Version): 0.99-6 released to CRAN
1453 :    
1454 : bates 1119 * src/dgBCMatrix.c (cscb_trcbsm): Fix due to Peter Dalgaard for
1455 :     segfault in cases with multiple non-nested grouping factors.
1456 :    
1457 : maechler 1109 2006-01-03 Martin Maechler <maechler@stat.math.ethz.ch>
1458 :    
1459 :     * DESCRIPTION (Version): 0.99-4 to be released to CRAN
1460 :     (Depends): also on 'utils'
1461 :    
1462 :     * R/AllClass.R (diagonalMatrix): new class with "ddi*" and "ldi*"
1463 :     * R/diagMatrix.R (Diagonal): constructor and methods for
1464 :     diagonal matrices
1465 :    
1466 :     * R/ltTMatrix.R: new "minimal methods"
1467 :    
1468 : maechler 1091 2005-12-12 Martin Maechler <maechler@stat.math.ethz.ch>
1469 :    
1470 :     * R/AllGeneric.R (tcrossprod): 2-argument version; here, and for
1471 :     all methods (and help files).
1472 :    
1473 : maechler 1084 2005-12-09 Martin Maechler <maechler@stat.math.ethz.ch>
1474 :    
1475 :     * R/Auxiliaries.R (dimNamesCheck): fixed thinko -> bug
1476 :     for case (dimn. op no_dimn.)
1477 :    
1478 :     2005-11-14 Douglas Bates <bates@stat.wisc.edu>
1479 :    
1480 : maechler 1174 * DESCRIPTION (Version): 0.99-2 released to CRAN
1481 : maechler 1084
1482 : bates 988 2005-10-21 Douglas Bates <bates@stat.wisc.edu>
1483 :    
1484 :     * R/lmer.R (simulate method): Fixed a drop=FALSE problem reported
1485 :     by Julian Faraway.
1486 :    
1487 : maechler 976 2005-10-06 Martin Maechler <maechler@stat.math.ethz.ch>
1488 :    
1489 :     * R/Auxiliaries.R (try_as): new utility
1490 :     * R/sparseMatrix.R: use try_as() in coercion to original class
1491 :    
1492 : maechler 956 2005-09-30 Martin Maechler <maechler@stat.math.ethz.ch>
1493 :    
1494 :     * src/dgCMatrix.c (double_to_csc): and dgeMatrix_to_csc()
1495 :    
1496 :     2005-09-29 Martin Maechler <maechler@stat.math.ethz.ch>
1497 :    
1498 :     * R/Auxiliaries.R (dimNamesCheck): added
1499 :    
1500 :     * R/Matrix.R (as.array), (as.vector): new
1501 :    
1502 : maechler 954 2005-09-28 Martin Maechler <maechler@stat.math.ethz.ch>
1503 :    
1504 :     * R/Matrix.R (Matrix): get logical argument 'sparse' with a smart
1505 : maechler 956 default.
1506 :     * R/AllClass.R: move 'factors' slot toplevel "Matrix";
1507 :     "pMatrix" now contains "sparseMatrix"
1508 : maechler 954
1509 : maechler 948 2005-09-26 Martin Maechler <maechler@stat.math.ethz.ch>
1510 :    
1511 :     * tests/Class+Meth.R: new tests; t(t(m)) == m
1512 :    
1513 :     * src/dtCMatrix.c (tsc_transpose): add forgotten "diag" slot
1514 :    
1515 :     * src/dsTMatrix.c (dsTMatrix_as_dsCMatrix): bad typo (segfault!)
1516 :     * src/dtTMatrix.c (dtTMatrix_as_dtCMatrix): new
1517 :    
1518 :     * R/dspMatrix.R: typo in "t" method
1519 :    
1520 : maechler 925 2005-09-18 Douglas Bates <bates@wisc.edu>
1521 :    
1522 :     * R/AllClass.R (TsparseMatrix), CsparseM* and RsparseM*
1523 :     * R/Tsparse.R: instead of R/gTMatrix.R
1524 :     * R/Csparse.R: new
1525 :     * src/Tsparse.c (Tsparse_to_Csparse): new; -> cholmod_()
1526 :     * src/Tsparse.c: new; many trivial methods calling cholmod_()
1527 :     * src/Csparse.c (Csparse_to_Tsparse), transpose, (mat|cross)prod:
1528 :     via cholmod
1529 :    
1530 :     2005-09-16 Martin Maechler <maechler@stat.math.ethz.ch>
1531 :    
1532 :     * R/Auxiliaries.R (non0ind): new function using new C code
1533 :     * src/dgCMatrix.c (compressed_non_0_ij): new utility
1534 :    
1535 : bates 917 2005-09-15 Douglas Bates <bates@localhost.localdomain>
1536 :    
1537 :     * src/chm_common.h: header file required by all C sources that
1538 : maechler 1174 call CHOLMOD functions. It defines a cholmod_common structure
1539 : bates 917 called 'c' whose address is passed as the last argument to
1540 :     (virtually) every CHOLMOD function.
1541 :    
1542 :     * src/Pattern.c: Simple example of the use of CHOLMOD.
1543 :    
1544 :     * src/init.c: initialize and finalize the cholmod_common structure.
1545 :    
1546 :     * src/Makefile: Added source packages CHOLMOD UMFPACK AMD COLAMD
1547 :     LDL and CCOLAMD from the U. of Florida sparse matrix library.
1548 :    
1549 : maechler 908 2005-09-08 Martin Maechler <maechler@stat.math.ethz.ch>
1550 :    
1551 :     * inst/test-tools.R: new file collecting the utility functions used
1552 :     in ./tests/*.R
1553 :    
1554 :     * R/ddenseMatrix.R (cbind2): new methods for "numeric" and "matrix"
1555 :     * R/Matrix.R (cbind2): methods for NULL and missing
1556 :    
1557 : maechler 886 2005-08-31 Martin Maechler <maechler@stat.math.ethz.ch>
1558 :    
1559 :     * R/AllClass.R: new "index" class for "[" and "[<-":
1560 :     First cut at "symmetricMatrix" and "triangularMatrix"
1561 :     * R/gTMatrix.R (.ind.prep): new function;
1562 : maechler 1174 Logical and character indexing now work too.
1563 : maechler 886 * R/Matrix.R: cheap "[<-" methods for denseMatrix now work
1564 :     * tests/indexing.R: new, including *.Rout.save
1565 :     * tests/dgTMatrix.R: new
1566 :    
1567 : bates 876 2005-08-29 Douglas Bates <bates@wisc.edu>
1568 :    
1569 :     * src/dgTMatrix.c (graphNEL_as_dgTMatrix): Corrected the position
1570 :     indicator pos not being updated. Also enforced upper triangular
1571 :     for symmetric case. Need to coerce edges component of elements of
1572 :     edge list - grr! (Why don't they define their classes cleanly?)
1573 :    
1574 : maechler 871 2005-08-26 Martin Maechler <maechler@stat.math.ethz.ch>
1575 :    
1576 :     * R/Matrix.R: added first "[<-" methods; not yet functional
1577 : bates 1352 * R/denseMatrix.R: ditto
1578 : maechler 871 * man/Subassign-methods.Rd: new help file for these
1579 :    
1580 :     2005-08-25 Martin Maechler <maechler@stat.math.ethz.ch>
1581 :    
1582 :     * DESCRIPTION (Version): 0.98-6
1583 :    
1584 :     * R/denseMatrix.R: new file for "[" fallback methods for all dense
1585 :     matrices.
1586 :    
1587 : maechler 868 2005-08-19 Martin Maechler <maechler@stat.math.ethz.ch>
1588 :    
1589 :     * src/lgCMatrix.c (lcsc_to_matrix): new; need for
1590 :     as( <logical>, "matrix")
1591 :    
1592 :     * R/pMatrix.R: coercion to "lgTMatrix"
1593 :    
1594 :     * R/gTMatrix.R: new virtual class to define "[" methods for.
1595 :     * man/gTMatrix-class.Rd:
1596 :     * General slight re-organization of where "[" methods are defined.
1597 :     more to come.
1598 :    
1599 : maechler 871 2005-08-18 Douglas Bates <bates@wisc.edu>
1600 : maechler 868
1601 : maechler 1174 * DESCRIPTION (Version): 0.98-5 released to CRAN
1602 : maechler 871
1603 :     * src/dgTMatrix.c (graphNEL_as_dgTMatrix): add first graphNEL methods
1604 :     * .....
1605 :    
1606 : bates 863 2005-08-18 Douglas Bates <bates@localhost.localdomain>
1607 :    
1608 :     * R/lmer.R: Corrected naming scheme in mcmcsamp to work with lmer
1609 :     or glmer objects.
1610 :    
1611 : maechler 860 2005-08-17 Martin Maechler <maechler@stat.math.ethz.ch>
1612 :    
1613 :     * DESCRIPTION (Version): 0.98-4 : upload to CRAN
1614 :    
1615 :     2005-08-16 Douglas Bates <bates@localhost.localdomain>
1616 :    
1617 :     * R/HBMM.R: finish re-writing R-only code.
1618 :    
1619 : bates 854 2005-08-15 Douglas Bates <bates@localhost.localdomain>
1620 :    
1621 :     * man/externalFormats.Rd: move documentation for writeHB and
1622 :     writeMM here.
1623 :    
1624 :     * src/mmio.c: replace inclusion of <malloc.h> by <stdlib.h>
1625 :     (suggested by Paul Roecker).
1626 :    
1627 :     * tests/validObj.R (assertError): Comment out test that is failing
1628 :     after recent changes in r-devel.
1629 :    
1630 : maechler 860
1631 : maechler 848 2005-08-11 Martin Maechler <maechler@stat.math.ethz.ch>
1632 :    
1633 :     * R/AllClass.R: intermediate virtual class "denseMatrix"
1634 :     * man/denseMatrix-class.Rd
1635 :     * NAMESPACE: export it, and also export
1636 :     * man/unused-classes.Rd: "iMatrix", "zMatrix" and "ldenseMatrix"
1637 :    
1638 : bates 846 2005-08-10 Douglas Bates <bates@wisc.edu>
1639 :    
1640 : maechler 848 * DESCRIPTION (Version): 0.98-3 to CRAN
1641 :    
1642 : bates 846 * src/dtrMatrix.c (dtrMatrix_validate): fixed up validation and
1643 :     matrix_solve code (which was really, really wrong).
1644 :    
1645 : bates 835 2005-08-07 Douglas Bates <bates@wisc.edu>
1646 : maechler 834
1647 :     * DESCRIPTION (Version): 0.98-2
1648 :    
1649 :     * R/HBMM.R (readHB), (readMM): read Matrix Market formats
1650 :    
1651 :     * R/lmer.R (abbrvNms): new
1652 :     * R/lmer.R (mcmcsamp): allow transformed parameters
1653 : bates 835 * src/HBMM.c (Matrix_writeMatrixMarket): Added read/write routines
1654 :     for the Harwell-Boeing and the MatrixMarket formats.
1655 : maechler 834
1656 :     2005-08-04 Martin Maechler <maechler@stat.math.ethz.ch>
1657 :    
1658 :     * man/dtrMatrix-class.Rd: add examples
1659 : bates 835 * man/dtpMatrix-class.Rd: ditto; plus note about PROBLEM
1660 : maechler 834
1661 :     * TODO: note the dtpMatrix (docu) bug
1662 :    
1663 :     * R/zzz.R (.onLoad): assignInNamespace("as.matrix", *, "base")
1664 :     in order to ensure that new as.matrix() is used by old functions,
1665 :     e.g., svd(), qr(), eigen(), dist(),..;
1666 :     apply(), also matplot() or pairs().
1667 :    
1668 :    
1669 :     2005-08-03 Martin Maechler <maechler@stat.math.ethz.ch>
1670 :    
1671 :     * R/lmer.R: add 'fixme' comments and move the linear vs glm check;
1672 :     add comments about 'control' / lmerControl() arguments
1673 :    
1674 : bates 835 2005-07-27 Douglas Bates <bates@wisc.edu>
1675 : bates 820
1676 : bates 835 * man/sleepstudy.Rd: Added the sleep data set.
1677 : maechler 1174 * DESCRIPTION (Version): 0.98-1 released to CRAN
1678 : bates 820
1679 : bates 835 2005-07-12 Douglas Bates <bates@wisc.edu>
1680 : maechler 834 * man/sleepstudy.Rd: Added the sleep data set.
1681 :    
1682 : bates 809 * R/lmer.R (glmmMCMC): Added PACKAGE = "Matrix" in a couple of
1683 :     .Call calls that were producing spurious output.
1684 :    
1685 : bates 835 2005-07-05 Douglas Bates <bates@wisc.edu>
1686 : bates 801
1687 :     * R/lmer.R (lmer): stored updated variance component estimates in
1688 :     mer object for the generalized model. (Bug reported by Renaud
1689 :     Lancelot).
1690 :    
1691 : bates 835 2005-07-03 Douglas Bates <bates@wisc.edu>
1692 : bates 794
1693 :     * src/lmer.c (glmer_devAGQ): Added AGQ for single grouping factor,
1694 :     unidimensional case.
1695 :    
1696 : bates 835 2005-06-08 Douglas Bates <bates@wisc.edu>
1697 : maechler 791
1698 :     * DESCRIPTION (Version): 0.96-1
1699 :    
1700 : maechler 1174 * moved lmer-class' R and C code moved from lme4 to here
1701 : maechler 791
1702 : bates 835 2005-06-04 Douglas Bates <bates@wisc.edu>
1703 : bates 763
1704 :     * R/dgCMatrix.R: Call to csc_matrix_mm used undefined arguments
1705 :     (reported by Guissepe Ragusa <gragusa@ucsd.edu>)
1706 :    
1707 : bates 835 2005-06-02 Douglas Bates <bates@wisc.edu>
1708 : bates 763
1709 :     * src/Makefile.win: Forgot to update this when Makefile changed.
1710 :    
1711 : bates 835 2005-05-11 Douglas Bates <bates@wisc.edu>
1712 : bates 726
1713 :     * src/dgCMatrix.c (csc_transpose): Simplified function fixing a
1714 :     bug reported by Kurt Hornik and Michael Hahsler.
1715 :    
1716 : bates 835 2005-05-10 Douglas Bates <bates@wisc.edu>
1717 : bates 725
1718 :     * src/lgCMatrix.c (Matrix_lgClgCmm): Implementation of methods for
1719 :     logical sparse matrices. These will also be used in the symbolic
1720 :     analysis for lmer objects.
1721 :    
1722 :     * src/dsCMatrix.c (dsCMatrix_matrix_solve): Copied the dimensions
1723 :     of b to the result. Fixes bug reported by Jean.Coursol@math.u-psud.fr
1724 : maechler 791
1725 : bates 835 2005-05-06 Douglas Bates <bates@wisc.edu>
1726 : bates 714
1727 :     * src/dgeMatrix.c (dgeMatrix_colsums): Added an implementation of
1728 :     colMeans, colSums, rowMeans and rowSums.
1729 :    
1730 : bates 835 2005-04-18 Douglas Bates <bates@wisc.edu>
1731 : bates 692
1732 :     * src/lgCMatrix.[ch]: code for _validate method and stub for
1733 :     multiplication operation.
1734 :    
1735 :     * src/dgeMatrix.c (dgeMatrix_matrix_solve): Passing wrong argument
1736 :     to dgetrs.
1737 :    
1738 :     * src/init.c: Fix cut-and-paste error in definition of
1739 :     dgeMatrix_matrix_solve
1740 :    
1741 :     * src/{many files}: Tighten code by using ALLOC_SLOT.
1742 :    
1743 : bates 835 2005-04-15 Douglas Bates <bates@wisc.edu>
1744 : bates 692
1745 :     * R/AllClass.R: Add lgTMatrix and lgCMatrix classes
1746 :    
1747 :     * DESCRIPTION: Eliminate import of stats.
1748 :    
1749 : maechler 791
1750 : bates 835 2005-04-06 Douglas Bates <bates@wisc.edu>
1751 : bates 692
1752 :     * R/AllClass.R : add logical sparse matrix classes
1753 :    
1754 : maechler 687 2005-04-01 Martin Maechler <maechler@stat.math.ethz.ch>
1755 :    
1756 :     * R/dgTMatrix.R: add "[" method for triplet matrices
1757 :     * R/sparseMatrix.R: and other sparse ones; --> add show() for sparse
1758 :    
1759 : bates 835 2005-03-31 Douglas Bates <bates@wisc.edu>
1760 : maechler 687
1761 :     * DESCRIPTION (Version): release 0.95-5 to CRAN
1762 :    
1763 :     * R/dMatrix.R: add %*%, crossprod and solve "fallback" methods
1764 :     * R/sparseMatrix.R: %*%, crossprod()
1765 :     * R/dgeMatrix.R: more "fallback" methods for numeric/dense matrices
1766 :     * man/*.Rd: move method definitions to 'Matrix' and 'dMatrix'
1767 :     * src/lmer.c (lmer_fitted): fix thinko
1768 :    
1769 : maechler 676 2005-03-26 Martin Maechler <maechler@stat.math.ethz.ch>
1770 :    
1771 :     * R/AllClass.R: add two virtual sparse classes ``on top''
1772 :    
1773 :     2005-03-24 Martin Maechler <maechler@stat.math.ethz.ch>
1774 :    
1775 :     * R/AllClass.R (setClass): use "VIRTUAL" for the virtual classes;
1776 :     correspondingly fix examples and tests/ since new()
1777 :     doesn't work for virtual classes.
1778 :    
1779 : maechler 658 2005-03-17 Martin Maechler <maechler@stat.math.ethz.ch>
1780 :    
1781 :     * R/Matrix.R (as.matrix): method and one for unname()
1782 :     * tests/dpoMatrix.R: tests should now be less platform dependent;
1783 :     also run for R 2.1.0; using as.matrix()
1784 :    
1785 : bates 835 2005-03-15 Douglas Bates <bates@wisc.edu>
1786 : maechler 658
1787 :     * R/pMatrix.R: "pMatrix" class added
1788 :     * ....
1789 :    
1790 : bates 835 2005-03-14 Douglas Bates <bates@wisc.edu>
1791 : bates 645
1792 :     * R/dtpMatrix.R: Add unpack method and an example.
1793 :    
1794 :     * src/dsyMatrix.c (dsyMatrix_trf): Add BunchKaufman factorization
1795 :     of general symmetric matrices and associated S4 methods.
1796 :    
1797 : maechler 658 2005-03-10 Martin Maechler <maechler@stat.math.ethz.ch>
1798 :     +
1799 :     2005-03-05 Martin Maechler <maechler@stat.math.ethz.ch>
1800 :    
1801 :     * R/dgeMatrix.R (setAs): and many other files: more coercion,
1802 :     crossprod() and "%*%" methods added; tests, too.
1803 :     * tests/matprod.R: new, for testing these
1804 :    
1805 : bates 835 2005-03-03 Douglas Bates <bates@wisc.edu>
1806 : bates 599
1807 :     * src/lmer.c (lmer_fitted): Added.
1808 :    
1809 : bates 835 2005-03-02 Douglas Bates <bates@wisc.edu>
1810 : bates 596
1811 :     * R/dsTMatrix.R: Conversion from dsTMatrix to dsCMatrix
1812 :    
1813 : bates 835 2005-02-28 Douglas Bates <bates@wisc.edu>
1814 : bates 582
1815 :     * src/*.c,po/,inst/po: Internationalization and localization of
1816 :     the package.
1817 :    
1818 :     * src/ldl.[ch]: Removed these as their contents are referenced in the
1819 :     R_ldl.c file.
1820 :    
1821 :     * src/flame.[ch]: Removed these source files.
1822 : maechler 658
1823 : bates 582 * src/dtrMatrix.c (make_array_triangular): Move to Mutils
1824 :    
1825 :     * src/LU.[ch],src/init.c: absorb in factorizations
1826 :    
1827 :     * src/Mutils.h: prepare for internationalization
1828 :    
1829 :     * src/cblas.h: move the enum definitions to Mutils.h and remove
1830 :     this file
1831 :    
1832 : maechler 578 2005-02-26 Martin Maechler <maechler@stat.math.ethz.ch>
1833 :    
1834 : maechler 579 * R/dgeMatrix.R: provide "dimnames" and "dimnames<-" methods
1835 :    
1836 :     * R/dtrMatrix.R: fix t() method
1837 :    
1838 : maechler 578 * R/dgeMatrix.R: define group methods "Arith", "Math", "Math2"
1839 : maechler 658 * NAMESPACE: export them (and import generics from "methods")
1840 : maechler 578 * tests/group-methods.R : and test them.
1841 :    
1842 :     * src/dtrMatrix.c (dtrMatrix_as_dgeMatrix): prevent seg.fault in
1843 :     border case
1844 :    
1845 :     2005-02-24 Douglas Bates <bates@stat.wisc.edu>
1846 :    
1847 : maechler 658 * DESCRIPTION (Version): 0.95-2 released to CRAN
1848 : maechler 578
1849 :     * src/dgBCMatrix.c:
1850 :     * src/lmer.c: many changes
1851 :     * ...
1852 :    
1853 : maechler 512 2005-02-04 Martin Maechler <maechler@stat.math.ethz.ch>
1854 :    
1855 :     * R/Matrix.R: add more sophisticated show() method.
1856 :    
1857 : maechler 578 2005-02-02 Douglas Bates <bates@stat.wisc.edu>
1858 :    
1859 :     * */* : almost complete reorganization of classes.
1860 :    
1861 : bates 835 2005-01-26 Douglas Bates <bates@wisc.edu>
1862 : bates 460
1863 :     * R/AllGeneric.R: Added matrix exponential generic expm and a method
1864 :     for the geMatrix class.
1865 :    
1866 : bates 835 2005-01-24 Douglas Bates <bates@wisc.edu>
1867 : bates 460
1868 :     * src/Makefile (clean): Remove *.a and *.so
1869 :    
1870 :     * man/cscBlocked-class.Rd: Remove reference to the lmer-class.
1871 :    
1872 : bates 835 2005-01-23 Douglas Bates <bates@wisc.edu>
1873 : bates 460
1874 : maechler 658 * src/lmer.c (Lind): Definition of Lind was backwards. This only
1875 : bates 460 had an effect in cases with more than 2 grouping factors.
1876 :    
1877 : bates 835 2005-01-03 Douglas Bates <bates@wisc.edu>
1878 : bates 415
1879 :     * src/lmeRep.c (lmer_variances): change from lmeRep to lmer
1880 :    
1881 : bates 835 2004-12-23 Douglas Bates <bates@wisc.edu>
1882 : bates 410
1883 :     * src/init.c (R_init_Matrix): Reorder calls to R_registerRoutines
1884 :     and R_useDynamicSymbols (suggested by B.D.Ripley).
1885 :    
1886 : bates 835 2004-12-14 Douglas Bates <bates@wisc.edu>
1887 : bates 392
1888 :     * R/sscMatrix.R: Add determinant methods
1889 :    
1890 :     * src/triplet.[ch],src/init.c (triplet_to_matrix): Add a coercion
1891 :     for tripletMatrix to matrix.
1892 :    
1893 : bates 835 2004-12-13 Douglas Bates <bates@wisc.edu>
1894 : bates 388
1895 : bates 392 * R/AllClass.R (.onLoad): Eliminate the bbCrosstab class, which is
1896 :     no longer used.
1897 :    
1898 : bates 388 * src/R_ldl.c: Created an R-specific version of the ldl.[ch] files
1899 :     with dynamic allocation of scratch arrays.
1900 :    
1901 :     * src/ssclme.c (ssclme_copy_ctab): Fixed bug in creation of ZtZ
1902 :     for multivariate random effects with multiple grouping factors.
1903 :     Fixes part but not all of #15.
1904 :    
1905 : bates 835 2004-12-03 Douglas Bates <bates@wisc.edu>
1906 : bates 375
1907 :     * src/lmeRep.c (lmeRep_factor): order of operations for multiple
1908 :     scalar grouping factors corrected.
1909 :    
1910 : bates 835 2004-11-29 Douglas Bates <bates@wisc.edu>
1911 : bates 375
1912 :     * src/bCrosstab.c: remove diag_update which is no longer used
1913 :    
1914 : bates 835 2004-11-16 Douglas Bates <bates@wisc.edu>
1915 : bates 350
1916 :     * src/Metis_utils.c: Move metis.h include to C sources so that the
1917 :     .h file can be included.
1918 :    
1919 : bates 835 2004-11-12 Douglas Bates <bates@wisc.edu>
1920 : bates 342
1921 : bates 350 * src/LU.c,geMatrix.c,trMatrix.c, etc.:
1922 : bates 342 Complete allocation of slots in NEW_OBJECT.
1923 :    
1924 :     * src/Mutils.h: Moved list of symbols to an include file
1925 :    
1926 : bates 835 2004-11-11 Douglas Bates <bates@wisc.edu>
1927 : bates 342
1928 :     * src/geMutils.c (Matrix_init): remove unused function
1929 :    
1930 : bates 835 2004-11-10 Douglas Bates <bates@wisc.edu>
1931 : bates 342
1932 :     * src/cscMatrix.c (csc_to_imagemat): removed unused function
1933 :    
1934 : bates 835 2004-11-05 Douglas Bates <bates@wisc.edu>
1935 : bates 327
1936 :     * src/Makefile.win (SOURCES_C): Keep consistent with Makefile
1937 :    
1938 : bates 835 2004-10-27 Douglas Bates <bates@wisc.edu>
1939 : bates 303
1940 :     * R/pdmatrix.R: remove PACKAGE="Matrix" in .Call calls
1941 :    
1942 : bates 835 2004-10-04 Douglas Bates <bates@wisc.edu>
1943 : bates 296
1944 :     * src/init.c: Created R_init_Matrix and added registration of C
1945 :     routines.
1946 :    
1947 : bates 835 2004-10-02 Douglas Bates <bates@wisc.edu>
1948 : bates 283
1949 :     * R/tripletMatrix.R: Force a require(lattice) for the image methods.
1950 :    
1951 : bates 835 2004-06-15 Douglas Bates <bates@wisc.edu>
1952 : bates 229
1953 :     * man/trMatrix-class.Rd: Escape the % chars in .Rd files.
1954 :    
1955 : bates 111 2004-04-20 Douglas Bates <bates@stat.wisc.edu>
1956 :    
1957 :     * src/Makefile.win ($(SHLIB)): Modifications per Uwe Ligges.
1958 :    
1959 : bates 109 2004-04-19 Douglas Bates <bates@stat.wisc.edu>
1960 :    
1961 :     * src/ssclme.c (ssclme_update_mm): fix logic error in
1962 :     ssclme_update_mm
1963 :    
1964 : bates 105 2004-04-18 Douglas Bates <bates@stat.wisc.edu>
1965 :    
1966 :     * src/ssclme.c (ssclme_coef, ssclme_coefGets): Create consistency
1967 :     in the order of unconstrained and constrained parameters.
1968 :     (ssclme_gradient): Added the gradients (not yet correct for
1969 :     multidimensional, unconstrained case).
1970 :    
1971 : bates 78 2004-04-14 Douglas Bates <bates@stat.wisc.edu>
1972 :    
1973 :     * src/ssclme.c (ssclme_EMsteps): Fix logic in REML update
1974 :    
1975 :     * src/Makefile.win: Remove unneeded ranlib call
1976 :    
1977 : bates 71 2004-04-12 Douglas Bates <bates@stat.wisc.edu>
1978 :    
1979 :     * DESCRIPTION (Version): New release
1980 :    
1981 :     * src/Makefile.win: Update Makefile.win to umfpack removal.
1982 :    
1983 : bates 49 2004-04-05 Douglas Bates <bates@bates2_home>
1984 :    
1985 :     * src/triplet_to_col.c: Create triplet_to_col as a native
1986 : maechler 658 function, not the version from umfpack. There were problems with
1987 : bates 49 the configuration of UMFPACK for 64-bit processors and there was
1988 :     only one umfpack routine being used so I moved it here.
1989 :    
1990 : bates 45 2004-04-04 Douglas Bates <bates@bates2_home>
1991 :    
1992 :     * src/ssclme.c (ssclme_variances): New function.
1993 :    
1994 : bates 28 2004-03-28 Douglas Bates <bates@bates2_home>
1995 :    
1996 :     * src/ssclme.c (ssclme_fitted): Added function.
1997 :    
1998 : bates 22 2004-03-27 Douglas Bates <bates@bates2_home>
1999 :    
2000 :     * src/ssclme.c (ssclme_transfer_dimnames): Add new function to
2001 :     store the dimnames in the XtX and bVar slots
2002 :     (ssclme_update_mm): Change the dimensions of the bVar slot
2003 :     components and the returned value from ssclme_ranef.
2004 :    
2005 : bates 10 2004-03-18 Douglas Bates <bates@stat.wisc.edu>
2006 :    
2007 :     * R/{pdMat.R,pdIdent.R,pdLogChol.R,pdMatrixLog.R,pdNatural.R},
2008 :     src/{pdMat.c,pdIdent.c,pdLogChol.c,pdNatural.c},
2009 :     tests/{pdCompSymm.R,pdDiag.R,pdIdent.R,pdLogChol.R,pdNatural.R},
2010 :     man/{pdMat-class.Rd,pdmatrix-class.Rd,corrmatrix-class.Rd,
2011 :     pdDiag-class.Rd,pdIdent-class.Rd,pdNatural-class.Rd,
2012 :     pdLogChol-class.Rd,coefGets.Rd,pdCompSymm-class.Rd,
2013 :     pdfactor-class.Rd,pdFactor.Rd,pdMatrix.Rd,
2014 :     pdBlocked-class.Rd},AllClass.R,AllGeneric.R:
2015 :     Moved the pdMat classes from the lme4 package.
2016 :    
2017 :     2004-03-02 Douglas Bates <bates@stat.wisc.edu>
2018 :    
2019 :     * man/ssclme-class.Rd: Update definition and documentation of the
2020 :     ssclme class to include the DIsqrt slot.
2021 :    
2022 :     * src/ssclme.c (ssclme_deviance): Modify order of computation
2023 :     (much faster using dsyrk, a level 3 BLAS routine).
2024 :    
2025 :     * src/Makefile (SUBLIBS): Change definition (K. Hornik)
2026 :    
2027 :     2004-02-28 Douglas Bates <bates@stat.wisc.edu>
2028 :    
2029 :     * tests/ssclme.R: Modify the test to account for the permutation
2030 :     of the levels of the grouping factors.
2031 :    
2032 :     2004-02-23 Douglas Bates <bates@stat.wisc.edu>
2033 :    
2034 :     * R/ssclme.R,src/ssclme.c (ssclme): Move slots of sscCrosstab slot
2035 :     directly into the ssclme class definition.
2036 :    
2037 :     2004-02-22 Douglas Bates <bates@stat.wisc.edu>
2038 :    
2039 :     * DESCRIPTION (Date): New release
2040 :    
2041 :     * man/ssclme-class.Rd: new file.
2042 :    
2043 :     * src/ssclme.c (ssclme_loglik): major revisions in design. It
2044 :     works and it's fast!
2045 :    
2046 :     2004-02-17 Douglas Bates <bates@stat.wisc.edu>
2047 :    
2048 :     * src/taucs/Makefile.win (lib): Change "ar" to "$(AR)" (B.Ripley)
2049 :    
2050 :     2004-02-16 Douglas Bates <bates@stat.wisc.edu>
2051 :    
2052 :     * DESCRIPTION (Date): New release
2053 :    
2054 :     * NAMESPACE: Don't export ssclme.
2055 :    
2056 :     * data/ScotsSec.rda, man/ScotsSec.Rd: Add Scottish secondary
2057 :     school data.
2058 :    
2059 :     2004-02-11 Douglas Bates <bates@stat.wisc.edu>
2060 :    
2061 :     * src/sscCrosstab.c (sscCrosstab): Added a row to the incidence to
2062 :     keep track of the fixed-effects and the response. Counts also
2063 :     gets an extra element, which is always one.
2064 :    
2065 :     * src/ldl.c: Include these routines from Tim Davis' LDL package.
2066 :    
2067 :     2004-02-10 Douglas Bates <bates@stat.wisc.edu>
2068 :    
2069 :     * src/cscMatrix.c (csc_transpose): new function
2070 :    
2071 :     * src/Mutils.c (csc_sort_columns): perm/iperm confusion corrected
2072 :     (csc_components_transpose): new function
2073 :    
2074 :     2004-02-06 Douglas Bates <bates@stat.wisc.edu>
2075 :    
2076 :     * src/triplet.c (triplet_validate): Fix Dim slot on generated
2077 :     triplets
2078 :    
2079 :     2004-01-30 Douglas Bates <bates@stat.wisc.edu>
2080 :    
2081 :     * R/sscCrosstab.R (sscCrosstab): Added sscCrosstab generator function.
2082 :    
2083 :     * src/LU.h (MATRIX_LU_H): Add #ifndef #define ... #endif to this
2084 :     and all other .h files in src.
2085 :    
2086 :     * src/Makefile.win: This and other Makefile.win files contributed
2087 :     by Brian Ripley.
2088 :    
2089 :     2004-01-27 Douglas Bates <bates@stat.wisc.edu>
2090 :    
2091 :     * R/syMatrix.R: Added methods for "%*%".
2092 :    
2093 :     * R/Hilbert.R (Hilbert): Changed Hilbert function to return a
2094 :     poMatrix object.
2095 :    
2096 :     2004-01-26 Douglas Bates <bates@stat.wisc.edu>
2097 :    
2098 :     * man/sscChol-class.Rd,man/mm.Rd,man/y.Rd: Added man pages.
2099 :    
2100 :     2004-01-25 Douglas Bates <bates@bates2_home>
2101 :    
2102 :     * inst/doc/Introduction.Rnw,Comparisons.Rnw: Added vignettes.
2103 :    
2104 :     * R/csc.R: Convert all cscMatrix classes to use Dim slot instead
2105 :     of nrow.
2106 :    
2107 :     2003-12-31 Douglas Bates <bates@stat.wisc.edu>
2108 :    
2109 :     * src/taucs/taucs.h: Moved taucs.h, amd.h, and umfpack.h into
2110 :     subdirectories.
2111 :    
2112 :     2003-12-08 Douglas Bates <bates@stat.wisc.edu>
2113 :    
2114 :     * src/taucs.h: Accidently referred to global header files
2115 :     instead of local files.
2116 :    
2117 :     2003-12-04 Douglas Bates <bates@stat.wisc.edu>
2118 :    
2119 :     * R/AllClass.R: Lots of changes. Removed all the lapack++ code
2120 :     and methods and replaced all classes with S4 classes.
2121 :    
2122 :     2003-04-19 Douglas Bates <bates@stat.wisc.edu>
2123 :    
2124 :     * R/det.R,man/det.Rd: Change name of det generic to determinant
2125 :    
2126 :     * src/R_LapackPP.cc: Change method of calculating determinants
2127 :    
2128 :     2003-02-03 Douglas Bates <bates@stat.wisc.edu>
2129 :    
2130 :     * DESCRIPTION (Version): removed empty data directory as requested
2131 :     by CRAN maintainers. Changed version number and date.
2132 :    
2133 :     2002-10-23 Douglas Bates <bates@stat.wisc.edu>
2134 :    
2135 :     * src/laindex.h: Applied patches from Brian Ripley for compilation
2136 :     under Windows.
2137 :    
2138 :     * Added configure.win and src/Makevars.win as requested by Brian
2139 :     Ripley.
2140 :    
2141 :     2002-05-03 Douglas Bates <bates@stat.wisc.edu>
2142 :    
2143 :     * src/lamatrix.h: Removing pre-1.2.0 compatibility code per Kurt
2144 :     Hornik.
2145 :    
2146 :     2002-04-24 Douglas Bates <bates@stat.wisc.edu>
2147 :    
2148 :     * configure.ac: Replaced configure.in with configure.ac
2149 :     contributed by Kurt Hornik.
2150 :    
2151 :     * aclocal.m4 (ac_clean_files): Replaced this with Kurt Hornik's
2152 :     version for R-1.5.0
2153 :    
2154 : maechler 512
2155 : bates 10 2001-12-10 Douglas Bates <bates@stat.wisc.edu>
2156 :    
2157 :     * man/eigen.Rd: Removed the .Alias in the example

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