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Annotation of /pkg/ChangeLog

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1 : maechler 1886 2007-06-07 Martin Maechler <maechler@stat.math.ethz.ch>
2 :    
3 :     * R/Auxiliaries.R (callGeneric): another fix, needed for some cases
4 :     of colSums(*, sparseResult = TRUE)
5 :    
6 : maechler 1883 2007-06-06 Martin Maechler <maechler@stat.math.ethz.ch>
7 :    
8 :     * R/lsparseMatrix.R, R/ldenseMatrix.R (all, any): change default to
9 :     'na.rm = FALSE' as "everywhere" else in R.
10 :    
11 : bates 1877 2007-06-05 Douglas Bates <bates@stat.wisc.edu>
12 :    
13 : bates 1878 * [r4421] src/CSparse_install.sh: Modify for new organization of
14 : maechler 1883 CSparse package
15 : bates 1877 * [r4425] src/UFsparse_download.sh: Update to version 3.0.0 of
16 :     SuiteSparse
17 :     * [r4426] src/Makefile: add ./UFconfig to the include path for
18 :     compilation
19 : maechler 1883 * [r4427] src/cs.[ch]: update to CSparse version 2.2.0
20 :     * [r4428] inst/doc/UFsparse/* src/{AMD,CHOLMOD,COLAMD}/*
21 :     src/UFconfig/UFconfig.h: Update to version 3.0.0 of SuiteSparse
22 :    
23 : maechler 1870 2007-06-05 Martin Maechler <maechler@stat.math.ethz.ch>
24 :    
25 :     * R/Auxiliaries.R (emptyColnames): + argument msg.if.not.empty, used in
26 :     * R/sparseMatrix.R (prSpMatrix): now gives a message about
27 :     suppressed column names.
28 :    
29 : bates 1868 2007-06-04 17:13 Douglas Bates <bates@stat.wisc.edu>
30 :    
31 :     * [r4418] src/Csparse.c, src/HBMM.c, src/Mutils.c, src/Mutils.h,
32 :     src/Tsparse.c, src/chm_common.c, src/chm_common.h, src/dgCMatrix.c,
33 :     src/dgeMatrix.c, src/dpoMatrix.c, src/dpoMatrix.h, src/dppMatrix.c,
34 :     src/dppMatrix.h, src/dsCMatrix.c, src/dspMatrix.c, src/dspMatrix.h,
35 :     src/dsyMatrix.c, src/dsyMatrix.h, src/dtpMatrix.c, src/dtrMatrix.c:
36 :     Remove warnings after change to const char* CHAR
37 :    
38 :     2007-06-04 17:11 Douglas Bates <bates@stat.wisc.edu>
39 :    
40 :     * [r4417] inst/include/Matrix_stubs.c, inst/include/cholmod.h: Corrected
41 :     type of M_cholmod_ssmult
42 :    
43 : bates 1863 2007-06-03 14:42 Douglas Bates <bates@stat.wisc.edu>
44 :    
45 :     * [r4412] inst/include/Matrix_stubs.c, inst/include/cholmod.h,
46 :     src/init.c: Yet another cholmod export - cholmod_ssmult
47 :    
48 : maechler 1855 2007-05-23 Martin Maechler <maechler@stat.math.ethz.ch>
49 :    
50 :     * NAMESPACE: exported drop0(), since
51 :     * man/drop0.Rd: I have seen several cases, I really wanted to use
52 :     it, so our users may want too.
53 :    
54 :     2007-05-22 Martin Maechler <maechler@stat.math.ethz.ch>
55 :    
56 :     * man/colSums.Rd: separately document colSums() etc, since these
57 :     have the extra argument 'sparseResult'.
58 :    
59 : maechler 1852 2007-05-21 Martin Maechler <maechler@stat.math.ethz.ch>
60 :    
61 :     * R/sparseMatrix.R (spMatrix): utility (T)sparse Matrix constructor;
62 :     * man/spMatrix.Rd: docu., including examples
63 :    
64 :     * R/Auxiliaries.R (sp.colMeans): etc, using a patched callGeneric(),
65 :     in order to make colMeans() etc fast *and* correct.
66 :     * R/sparseVector.R (replSPvec): "[<-" functionality for
67 :     sparseVectors; tested in
68 :     * tests/simple.R:
69 :    
70 :     2007-05-19 Martin Maechler <maechler@stat.math.ethz.ch>
71 :    
72 :     * R/sparseMatrix.R (print.sparseSummary): and summary() method for
73 :     (very) sparse Matrices; output similar to Matlab's print().
74 :    
75 : bates 1847 2007-05-17 Douglas Bates <bates@stat.wisc.edu>
76 :    
77 :     * src/HBMM.c (Matrix_writeMatrixMarket): Write 1-based, not
78 :     0-based, indices (Jose Quesada <quesada@gmail.com>).
79 :    
80 : bates 1844 2007-05-16 Douglas Bates <bates@stat.wisc.edu>
81 :    
82 :     * R/CHMfactor.R: Added solve methods for a CHMfactor object.
83 :    
84 : maechler 1845 2007-05-16 Martin Maechler <maechler@stat.math.ethz.ch>
85 :    
86 :     * R/Auxiliaries.R (sparsapply): new utility, much faster than
87 :     tapply1() for large sparse matrices.
88 :    
89 :     2007-05-15 Martin Maechler <maechler@stat.math.ethz.ch>
90 :    
91 :     * R/Matrix.R (dim<-): reshape now via sparseVector.
92 :    
93 :     * R/sparseVector.R: methods and function for
94 :     * R/AllClass.R: new "sparseVector" class and daughters.
95 :     * NAMESPACE: export new classes
96 :    
97 : maechler 1837 2007-05-14 Martin Maechler <maechler@stat.math.ethz.ch>
98 :    
99 :     * DESCRIPTION (Version): 0.99875-1
100 :     * src/Makefile.win: also remove Lapack code from here (cf. 04-25).
101 :    
102 : maechler 1834 2007-05-11 Martin Maechler <maechler@stat.math.ethz.ch>
103 :    
104 :     * R/Tsparse.R ([, Tsparse): fix last case: *duplicated*, symmetric
105 :     indexing
106 :     * tests/indexing.R: test set for that.
107 :    
108 : maechler 1833 2007-05-08 Martin Maechler <maechler@stat.math.ethz.ch>
109 :    
110 :     * R/Tsparse.R (replTmat): fix the case of *duplicated* index
111 :     entries.
112 :     * tests/indexing.R(out): add regression test for it
113 :    
114 :     2007-04-30 Martin Maechler <maechler@stat.math.ethz.ch>
115 :    
116 :     * R/(l(dense|sparse))?Matrix.R (!): use 'x', not 'e1' as argument
117 :     name for "!" method definitions.
118 :    
119 : maechler 1829 2007-04-26 Martin Maechler <maechler@stat.math.ethz.ch>
120 :    
121 :     * R/Tsparse.R (intI): new utility, used for "[" :
122 :     Cleanup up there, and fixes for duplicated indices - more TODO!
123 :    
124 :     * tests/indexing.R(out): more tests
125 :    
126 : bates 1827 2007-04-25 Douglas Bates <bates@stat.wisc.edu>
127 :    
128 :     * DESCRIPTION,src/Makefile: require R>= 2.5.0 and remove Lapack
129 :     code that is now part of the R Lapack library.
130 : maechler 1829
131 : bates 1827 * src/init.c,inst/include/{Matrix_stubs.c,cholmod.h}:export
132 :     cholmod_factorize_p (used in lme4 for GLMMs and NLMMs).
133 :    
134 : maechler 1829 2007-04-21 Martin Maechler <maechler@stat.math.ethz.ch>
135 :    
136 :     * R/Matrix.R (image): method for all Matrices, not just sparse ones.
137 :    
138 :     2007-04-17 Martin Maechler <maechler@stat.math.ethz.ch>
139 :    
140 :     * R/Auxiliaries.R (tapply1): unname(.) -> colSums() etc don't end
141 :     up with extraneous names '0'...'<n-1>'
142 :    
143 : maechler 1825 2007-04-12 Martin Maechler <maechler@stat.math.ethz.ch>
144 :    
145 :     * R/dgTMatrix.R (mat2dgT): care about NAs
146 :    
147 :     2007-04-11 Martin Maechler <maechler@stat.math.ethz.ch>
148 :    
149 :     * R/kronecker.R: triangularity preserving methods
150 :    
151 : maechler 1803 2007-03-27 Martin Maechler <maechler@stat.math.ethz.ch>
152 :    
153 :     * R/kronecker.R: new file collecting kronecker() methods in one
154 :     place. Goal: become much faster!
155 :    
156 : maechler 1799 2007-03-23 Martin Maechler <maechler@stat.math.ethz.ch>
157 :    
158 :     * src/dtCMatrix.c (dtCMatrix_solve): use the new code from Kasper
159 :     Kristensen based cs_spsolve() instead of _lsolve & _usolve which
160 :     can be much faster.
161 :    
162 :     * tests/matprod.R: add regression tests for these (upper & lower).
163 :    
164 :     2007-03-19 Martin Maechler <maechler@stat.math.ethz.ch>
165 :    
166 :     * R/Matrix.R (diff): method for our Matrices.
167 :    
168 :     * R/sparseMatrix.R (isDiagonal): check dim()!
169 :    
170 :     2007-03-17 Martin Maechler <maechler@stat.math.ethz.ch>
171 :    
172 :     * R/Matrix.R (dim<-): new method for "reshape()" built on a
173 :     proposal from Tamas Papp.
174 :    
175 :     2007-03-16 Martin Maechler <maechler@stat.math.ethz.ch>
176 :    
177 :     * R/AllGeneric.R: remove all if(!isGeneric(.)) clauses
178 :    
179 :     * R/zzz.R (.onLoad, .onUnload): do *not* leave bind_activation(TRUE);
180 : maechler 1803 rather define and export cBind() and rBind() only.
181 :     --> useRs *must* change code that used to have cbind()/rbind() !!
182 : maechler 1799
183 : maechler 1803 * R/bind.R: change tests from cbind() to cBind() and similarly to rBind()
184 :     * R/bind.Rout.save: ditto
185 : maechler 1799
186 : bates 1787 2007-02-16 Douglas Bates <bates@r-project.org>
187 :    
188 :     * DESCRIPTION (Date, Version): 0.9975-11 with new date
189 :     * src/dgCMatrix.c (R_to_CMatrix, compressed_to_TMatrix): remove
190 :     const modifier on declaration of the array 'valid'
191 :    
192 : bates 1786 2007-02-12 Douglas Bates <bates@stat.wisc.edu>
193 :    
194 :     * R/CHMfactor.R: Add image method (coercion to sparseMatrix).
195 :    
196 : maechler 1765 2007-02-05 Martin Maechler <maechler@stat.math.ethz.ch>
197 :    
198 : maechler 1768 * DESCRIPTION (Date, Version): 0.9975-10 with new date.
199 :    
200 : maechler 1767 * R/Ops.R (Arith): make sure Csparse o Csparse also works for e.g. ntCMatrix
201 :     * tests/simple.R: test the above and some of these coercions:
202 :    
203 :     * R/nsparseMatrix.R: coercing "Csparse" to "lsparseMatrix";
204 :     be careful to avoid infinite recursion, using new coercions in
205 :     * R/ngCMatrix.R and nsC... and ntC...
206 :     * R/lsparseMatrix.R: ditto
207 :    
208 : maechler 1765 * R/SparseM-conv.R: more conversion, notably for triplet matrices.
209 :    
210 : maechler 1767 * src/dgCMatrix.c (R_to_C_Matrix): port Doug's fix and
211 :     * R/Rsparse.R: reactivate .Call()s
212 : maechler 1765
213 : maechler 1767 * tests/Class+Meth.R: a bit more on actual classes
214 :    
215 :     2007-02-04 Douglas Bates <bates@stat.wisc.edu>
216 :    
217 :     * src/dgCMatrix.c (compressed_to_TMatrix): fix memory bug using strdup()
218 :    
219 : maechler 1760 2007-02-03 Martin Maechler <maechler@stat.math.ethz.ch>
220 : maechler 1758
221 :     * DESCRIPTION (Version): 0.9975-10 to upload
222 :    
223 : maechler 1760 * tests/Class+Meth.R (tstMatrixClass): require coercions to
224 :     specific classes less unconditionally.
225 :    
226 :     * R/Auxiliaries.R: get rid of as_Tsparse() and as_Rsparse()
227 :    
228 :     * R/Tsparse.R (triu): etc, use as(*, "TsparseMatrix") instead of as_Tsparse()
229 :    
230 :     * R/Rsparse.R (.R.2.T): R-level workaround using compressed_to_TMatrix.
231 : maechler 1758 * R/Rsparse.R (.R.2.C): R-level workaround since C-level
232 :     R_to_CMatrix segfaults on one platform.
233 : maechler 1760 Eliminate most coercion method to *specific* classes, and replace
234 :     with virtual classes coercions.
235 : maechler 1758
236 : maechler 1760
237 : maechler 1758 2007-02-01 Martin Maechler <maechler@stat.math.ethz.ch>
238 :    
239 :     * src/init.c: export the CHM...._validate() placeholders, since
240 :     they *are* called.
241 :    
242 : maechler 1760 * tests/Class+Meth.R (classCanCoerce): and starting to test
243 : maechler 1758 all as(<from>, <to>)
244 :    
245 : maechler 1751 2007-01-30 Martin Maechler <maechler@stat.math.ethz.ch>
246 :    
247 :     * R/Tsparse.R ([): more care when subsetting triangular Tsparse
248 :     * tests/indexing.R: tested now
249 :     * tests/indexing.Rout.save: updated
250 :    
251 :     * src/Csparse.c (Csparse_to_dense): use Rkind = -1 for PATTERN to
252 :     * src/chm_common.c (chm_dense_to_SEXP): return "ngeMatrix" when
253 :     appropriate.
254 :    
255 :     * NAMESPACE: export a trivial
256 :     * R/Matrix.R: drop() Matrix-method
257 :    
258 :     * R/AllClass.R: moved all prototypes to virtual super classes.
259 :    
260 :     * R/Rsparse.R: many more coercions to have less exceptions in
261 :     * tests/Class+Meth.R:
262 :    
263 :     * R/Ops.R (Compare): tweak for case with NA
264 :     * tests/simpl.R: hence another 'FIXME' eliminated
265 :    
266 : maechler 1747 2007-01-29 Martin Maechler <maechler@stat.math.ethz.ch>
267 :    
268 : maechler 1748 * R/diagMatrix.R (solve): the obvious methods for diagonalMatrix
269 :     objects.
270 :    
271 : maechler 1747 * tests/Class+Meth.R (tstMatrixClass): now testing diag(), nnzero(),
272 :     and more of "!", "&", "|", all, any; coercions
273 :    
274 :     * R/Rsparse.R: many coercions (which enable quite a few other
275 :     methods), thanks to enhancements in
276 :     * src/dgCMatrix.c (R_to_CMatrix): new, and
277 :     * src/dgCMatrix.c (compressed_to_TMatrix): now for (d,l,n) ,
278 :     symmetric & triangular and ..RMatrix objects.
279 :    
280 :     * src/TMatrix_as.c (Matrix_T_as_DENSE,Matrix_T_as_GENERAL):
281 :     renamed file from src/dsTMatrix.c;
282 :     now dealing with symmetric and triangular Tsparse coercions, both
283 :     to dense and general.
284 :    
285 :     2007-01-27 Martin Maechler <maechler@stat.math.ethz.ch>
286 :    
287 :     * src/dsTMatrix.c: has now "l" and "n" methods besides the "d" ones.
288 :    
289 :     * R/Ops.R (Arith): <dgCMatrix> o <numeric> now remains sparse
290 :     where sensible when the <numeric> is of length > 1.
291 :    
292 :     2007-01-26 Martin Maechler <maechler@stat.math.ethz.ch>
293 :    
294 :     * R/Matrix.R ([<-): for M[] <- value: fix length
295 :    
296 :     2007-01-25 Martin Maechler <maechler@stat.math.ethz.ch>
297 :    
298 :     * R/Auxiliaries.R (n2l_Matrix): new, to be used in
299 :     * R/ndenseMatrix.R: new coercions n* -> l*
300 :    
301 : maechler 1738 2007-01-22 Martin Maechler <maechler@stat.math.ethz.ch>
302 :    
303 :     * R/triangularMatrix.R: new file; simple triu() and tril() methods.
304 :    
305 :     * R/Ops.R ("Logic"): and other "Ops", many updates
306 :    
307 :     2007-01-18 Martin Maechler <maechler@stat.math.ethz.ch>
308 :    
309 :     * src/Mutils.h (SET_DimNames): new utility
310 :    
311 :     * R/Auxiliaries.R (nnzero): improved and now exported via
312 :    
313 :     * NAMESPACE: + nnzero(); length() == prod(dim(.)) method for all "Matrix" objects
314 :    
315 : maechler 1725 2007-01-17 Martin Maechler <maechler@stat.math.ethz.ch>
316 :    
317 :     * R/diagMatrix.R (!): fix typo.
318 :    
319 :     2007-01-16 Martin Maechler <maechler@stat.math.ethz.ch>
320 :    
321 :     * R/Auxiliaries.R (as_Csparse): and quite a few others:
322 :     allow to pass class definition --> speedup
323 :     * R/sparseMatrix.R: apply the above
324 :    
325 :     * R/Csparse.R: coercion Csparse* to dense* now preserves shape properties.
326 :    
327 :     * src/Mutils.h (mMatrix_as_geMatrix): new, based on
328 :     * src/Mutils.c (dup_mMatrix_as_geMatrix): new; generalization of
329 :     old dup_mMatrix_as_dgeMatrix), eliminating a long-standing "FIXME".
330 :    
331 :     * src/dense.c (dense_to_Csparse): use new mMatrix_as_geMatrix()
332 :    
333 :     * R/denseMatrix.R (.dense2C): based on dense_to_Csparse: name it,
334 :     and use it for "sparse*" as well, since it's faster than the
335 :     as_Csparse(.) way.
336 :    
337 :     2007-01-15 Martin Maechler <maechler@stat.math.ethz.ch>
338 :    
339 :     * R/Ops.R ("Logic"): more methods, notably an <lgC> o <lgC> one.
340 :    
341 : maechler 1724 2007-01-12 Martin Maechler <maechler@stat.math.ethz.ch>
342 :    
343 :     * R/Tsparse.R (.TM.repl.i.2col): new internal function to be used
344 :     as method for M[ ij ] <- v
345 :     * R/Csparse.R:: go via Tsparse for "M[ij] <- v"
346 :    
347 :     * R/Ops.R: "Compare" for (C|R)sparse: need pointer slot for all
348 :     FALSE answer
349 :    
350 :     * R/Csparse.R (replCmat): fix the "all non-zero" case with reordering
351 :     * tests/indexing.R: test it, and some of the above
352 :    
353 :     2007-01-05 Martin Maechler <maechler@stat.math.ethz.ch>
354 :    
355 :     * R/Auxiliaries.R (is_duplicatedT): new utility
356 :    
357 : bates 1716 2007-01-05 Douglas Bates <bates@stat.wisc.edu>
358 :    
359 :     * src/init.c (R_init_Matrix): export cholmod_scale
360 :    
361 : maechler 1724 2006-12-30 Martin Maechler <maechler@stat.math.ethz.ch>
362 :    
363 :     * R/zzz.R (tmp): for R >= 2.5.0, extend formals of our
364 :     base::as.matrix to (x, ...)
365 :    
366 : maechler 1714 2006-12-28 Martin Maechler <maechler@stat.math.ethz.ch>
367 :    
368 :     * R/Ops.R ("Arith" etc): move almost all "Ops" methods to new R
369 :     file; start using "Logic", hence
370 :    
371 :     * DESCRIPTION (Depends): R >= 2.4.1 (since we want "Logic")
372 :     * NAMESPACE: import and export "Logic"
373 :    
374 :     2006-12-27 Martin Maechler <maechler@stat.math.ethz.ch>
375 :    
376 :     * src/zpotfr.f and dependencies: use LAPACK 3.1 version
377 :     only needed previously to R version 2.5.0.
378 : maechler 1724
379 : maechler 1710 2006-12-26 Martin Maechler <maechler@stat.math.ethz.ch>
380 :    
381 :     * DESCRIPTION (Date, Version): 0.9975-8, ready for release
382 :    
383 :     * R/Tsparse.R (replTmat): fix subassignment of triangular
384 :     * R/Csparse.R (replCmat): ditto
385 :     * tests/indexing.R: more tests, incl the above fix
386 :    
387 :     2006-12-23 Martin Maechler <maechler@stat.math.ethz.ch>
388 :    
389 :     * R/Auxiliaries.R (drop0): extend for non CSparse
390 :     * R/Auxiliaries.R (diagU2N): should work for all sparseMatrix
391 :    
392 :     * src/Csparse.c (Csparse_to_Tsparse, Csparse_general_to_symmetric):
393 :     use uplo correctly (!); other places: use uplo_P() macro
394 :    
395 :     * R/Csparse.R (replCmat): call diagU2N() when needed
396 :     * R/Tsparse.R (replTmat): ditto
397 :    
398 :     * src/dtCMatrix.c (tCMatrix_validate): new
399 :     * src/dtTMatrix.c (tTMatrix_validate): new, used in
400 :     * R/AllClass.R: for validity of dtC, dsC, and dtT, dsT.
401 :    
402 :     * R/diagMatrix.R (replDiag): to use in [<-
403 :    
404 : maechler 1708 2006-12-22 Martin Maechler <maechler@stat.math.ethz.ch>
405 :    
406 :     * R/Auxiliaries.R (as_Csparse2, as_geSimpl): new functions;
407 :     also more general diagU2N().
408 :    
409 :     2006-12-21 Martin Maechler <maechler@stat.math.ethz.ch>
410 :    
411 :     * R/bind2.R: new file for all cbind2(), rbind() methods moved here
412 :     from R/<foo>Matrix.R files. Better diagonal & improved sparse methods.
413 :    
414 : maechler 1707 2006-12-20 Martin Maechler <maechler@stat.math.ethz.ch>
415 :    
416 :     * tests/bind.R: a few more cases
417 :     * R/Auxiliaries.R (.M.kind): also work for atomic vectors
418 :    
419 :     * R/denseMatrix.R (cbind2/rbind2): moved here (and generalized) from
420 :     * R/ddenseMatrix.R (cbind2/rbind2)
421 :     * R/Tsparse.R (replTmat): final(?!) fix for "[<-" ..
422 :     * tests/indexing.R
423 :     * tests/indexing.Rout.save: updated
424 :    
425 :     2006-12-18 Martin Maechler <maechler@stat.math.ethz.ch>
426 :    
427 :     * R/Tsparse.R (replTmat): fixed a remaining "[<-" bug in
428 :     * tests/indexing.R
429 :    
430 : maechler 1705 2006-12-15 Martin Maechler <maechler@stat.math.ethz.ch>
431 :    
432 :     * R/sparseMatrix.R (prSpMatrix): "." alignment much improved:
433 :     align with proper position of "0", i.e., right for integers.
434 :     argument 'align' by default is "fancy".
435 :    
436 :     2006-12-14 Martin Maechler <maechler@stat.math.ethz.ch>
437 :    
438 :     * R/sparseMatrix.R: delegate "Compare" to "Csparse.."
439 :     * R/Csparse.R: and fix "Compare" for more cases.
440 :     * tests/Class+Meth.R: test some of these (m == m, m != m)
441 :    
442 :     2006-12-13 Martin Maechler <maechler@stat.math.ethz.ch>
443 :    
444 :     * R/lsparseMatrix.R: all() and any() methods
445 :     * R/ldenseMatrix.R: ditto
446 :     * NAMESPACE, R/Matrix.R: ditto
447 :    
448 :     * man/all-methods.Rd: document them minimally
449 :    
450 :     * tests/simple.R: add a few examples for these
451 :    
452 : maechler 1696 2006-12-11 Martin Maechler <maechler@stat.math.ethz.ch>
453 :    
454 :     * R/Tsparse.R ([): fix long standing typo in symmetric case
455 :     * man/dsCMatrix-class.Rd: add example exhibiting the above case
456 :    
457 : bates 1691 2006-12-10 Douglas Bates <bates@stat.wisc.edu>
458 :    
459 :     * src/CHMfactor.c (CHMfactor_to_sparse): change LDL factorization
460 :     to LL before converting to a sparse matrix. (The LDL form can be
461 :     converted to a sparse matrix but it is implicitly a unit
462 :     triangular matrix and a diagonal matrix overwritten on the diagonal.)
463 :    
464 :     2006-12-09 Douglas Bates <bates@stat.wisc.edu>
465 :    
466 :     * src/chm_common.c (chm_factor_to_SEXP): allocate and fill the Dim slot.
467 :    
468 : bates 1688 2006-12-08 Douglas Bates <bates@stat.wisc.edu>
469 :    
470 :     * DESCRIPTION (Version): updated -> release 0.9975-7
471 :     * src/{init.c,chm_common.c}, inst/include/*: export cholmod_analyze_p
472 :    
473 : maechler 1682 2006-11-30 Martin Maechler <maechler@stat.math.ethz.ch>
474 :    
475 :     * R/diagMatrix.R (%*%): write a direct [diag o Csparse] method
476 :    
477 : bates 1681 2006-11-29 Douglas Bates <bates@stat.wisc.edu>
478 :    
479 :     * src/dgeMatrix.c (dgeMatrix_solve): Check error code from dgetri.
480 :     * tests/dg_Matrix.R: Add Barry Rowlingson's test of a matrix that
481 :     is exactly singular.
482 :    
483 : maechler 1674 2006-11-07 Martin Maechler <maechler@stat.math.ethz.ch>
484 :    
485 :     * DESCRIPTION (Date): updated -> release 0.9975-6
486 :    
487 : maechler 1673 2006-11-06 Martin Maechler <maechler@stat.math.ethz.ch>
488 :    
489 :     * R/Csparse.R (replCmat): symmetric indexing of symmetric matrix
490 :     now returns symmetric.
491 :    
492 :     * R/zzz.R ("diag<-"): replace "diag<-" in base for R <= 2.4.x
493 :    
494 :     * R/Matrix.R (.M.sub.i.2col): new, for M[ cbind(i,j) ] indexing.
495 :     * R/Matrix.R (.M.repl.i.2col): new, for M[ cbind(i,j) ] <- value
496 :    
497 :     * R/Auxiliaries.R (.type.kind): added
498 :    
499 :     2006-11-04 Martin Maechler <maechler@stat.math.ethz.ch>
500 :    
501 :     * src/cs.[ch]: updated to CSparse Version 2.0.3 by simply
502 :     running src/CSparse_install.sh
503 :    
504 :     * R/denseMatrix.R: "[": keep symmetric on symmetric indexing.
505 :    
506 : maechler 1665 2006-11-03 Martin Maechler <maechler@stat.math.ethz.ch>
507 :    
508 :     * src/dsCMatrix.c (dsCMatrix_Csparse_solve): new
509 :     * R/dsCMatrix.R (solve): "fully-sparse" using the above.
510 :    
511 :     * R/AllClass.R: "pMatrix" now also inherits from "generalMatrix"
512 :    
513 :     * tests/Class+Meth.R (tstMatrixClass): now assure
514 :     the (important in method programming) property :
515 :    
516 :     ###>> Every "Matrix" is either
517 :     ###>> "general*", "symmetric*", "triangular*" or "diagonal*"
518 :    
519 :     (where "*" stands for "Matrix")
520 :    
521 :     * R/Auxiliaries.R (diagU2N): now .Call()s Csparse_diagU2N for <Csparse>
522 :    
523 :     * R/dMatrix.R (Compare(<dMatrix>,<dMatrix>): update and
524 :     * tests/validObj.R: checks for "comparison"
525 :    
526 :     * R/sparseMatrix.R ([): improved indexing for sparse;
527 :     trying to keep <symmetric>[ n, n] symmmetric
528 :    
529 :     * tests/indexing.R: indexing for logical sparse now ok
530 :    
531 :    
532 : maechler 1660 2006-11-02 Martin Maechler <maechler@stat.math.ethz.ch>
533 :    
534 : maechler 1661 * src/Tsparse.c: use xTsparse_validate() , and hence remove
535 :    
536 :     * src/{ltC,lsC,lgT}Matrix.[ch]: removed
537 :    
538 :     2006-11-02 Martin Maechler <maechler@stat.math.ethz.ch>
539 :    
540 : maechler 1660 * R/AllClass.R (Matrix-class): check length of dimnames in validity.
541 :    
542 :     * tests/simple.R: validObject() checking the above.
543 :    
544 : maechler 1665 * src/dgCMatrix.c (xCMatrix_validate): new, small and simple,
545 : maechler 1660 replacing both dgCMatrix_validate and lgCM*.
546 :    
547 :     * src/Csparse.c (Csparse_dense_prod, etc): do not lose dimnames;
548 :     fix dimnames setting in other places.
549 :     * src/chm_common.c (chm_dense_to_SEXP): now can pass dimnames
550 :    
551 : maechler 1659 2006-11-01 Martin Maechler <maechler@stat.math.ethz.ch>
552 :    
553 : maechler 1660 * R/Csparse.R,src/Csparse.c, etc: tcrossprod(<CsparseM>,<CsparseM>)
554 :    
555 :     * R/sparseMatrix.R (isSymmetric): drop 'factors' slot for
556 :     symmetry test, via
557 : maechler 1659 * R/Auxiliaries.R (.as.dgC.0.factors):
558 :    
559 : bates 1657 2006-11-01 Douglas Bates <bates@r-project.org>
560 :    
561 :     * R/Csparse.R,src/Csparse.c,tests/matprod.R,
562 :     man/CsparseMatrix-class.Rd: crossprod(<CsparseMatrix>,
563 :     <CsparseMatrix>) added
564 :    
565 : maechler 1655 2006-10-30 Martin Maechler <maechler@stat.math.ethz.ch>
566 :    
567 :     * tests/matprod.R: add a variation of Harri's example
568 :    
569 :     * R/dsparseMatrix.R: fix crossprod(<dsparse>, <dge>) to *not*
570 :     recursive infinitely.
571 :    
572 :     * R/dgCMatrix.R: + solve(<sparse>, <sparse>)
573 :    
574 :     * tests/indexing.R: add test for the "<" bug fixed 10-27 in R/dMatrix.R
575 :    
576 :     2006-10-28 Martin Maechler <maechler@stat.math.ethz.ch>
577 :    
578 :     * tests/Class+Meth.R (tstMatrixClass): more: use non-trivial
579 :     matrix if possible; test m+m == 2*m; now test dgRMatrix.
580 :     * R/dgRMatrix.R (.to.dgR): a few more coercions, in order to
581 :     satisfy the above test.
582 :    
583 : maechler 1654 2006-10-27 Martin Maechler <maechler@stat.math.ethz.ch>
584 :    
585 : maechler 1655 * R/Matrix.R (Ops): <Matrix> o <matrix> method added
586 :    
587 : maechler 1654 * R/dgCMatrix.R: solve(a, b="missing") based on
588 :     * src/dgCMatrix.c (dgCMatrix_matrix_solve): extend to work with
589 :     RHS = NULL.
590 :    
591 :     * R/diagMatrix.R (diagdiagprod): extend %*% etc to ldiMatrix;
592 :     add more (needed) [t]crossprod() methods.
593 :    
594 :     * man/ddiMatrix-class.Rd: more info, notably on 'diag'
595 :    
596 :     * R/Auxiliaries.R (as_CspClass): cleanup
597 :     (drop0): internal utility for "Csparse_drop(*, 0)"
598 :     (.bail.out.2): encourage active feedback
599 :    
600 :     2006-10-26 Martin Maechler <maechler@stat.math.ethz.ch>
601 :    
602 :     * R/dMatrix.R(Compare): new(), then slots [no validity check]
603 :    
604 :     * src/Csparse.c (Csparse_validate): fixed (and more efficient in
605 :     non-valid or 'sorted' case).
606 :    
607 :     * R/dsparseMatrix.R: add "chol" method.
608 :     * R/ddenseMatrix.R: ditto
609 :    
610 :     * R/diagMatrix.R (Ops): group methods for <diagonal> o <sparse>
611 :     * NAMESPACE (Ops)
612 :     * R/diagMatrix.R (diag2T): simple utility used "higher level"
613 :     coercion; deprecating direct lower level coercions.
614 :    
615 :     * R/*.R (seq): use seq_len() and seq_along() where possible.
616 :    
617 :    
618 : maechler 1647 2006-10-23 Martin Maechler <maechler@stat.math.ethz.ch>
619 :    
620 :     * DESCRIPTION (Version): 0.9975-5 ready for release
621 :    
622 : bates 1646 2006-10-20 Douglas Bates <bates@stat.wisc.edu>
623 :    
624 :     * src/init.c (R_init_Matrix): export more cholmod CCallable functions.
625 :    
626 : maechler 1642 2006-10-20 Martin Maechler <maechler@stat.math.ethz.ch>
627 :    
628 :     * R/AllClass.R (corMatrix): add 'validity' check;
629 :     comment out unused "LDL" class definition
630 :     * NAMESPACE: mention, but do not export "LDL" class
631 :     * R/corMatrix.R: new (simple), needed for R-devel with
632 :     * tests/Class+Meth.R (tstMatrixClass): 1 exception for corMatrix
633 :     coerce and t() exceptions for all 5 'Mat.MatFact' classes.
634 :    
635 : bates 1641 2006-10-19 Douglas Bates <bates@stat.wisc.edu>
636 :    
637 :     * src/chm_common.h: Add R_cholmod_start to initialize cholmod to
638 :     use Rprintf and R's error handling.
639 :    
640 : maechler 1635 2006-10-17 Martin Maechler <maechler@stat.math.ethz.ch>
641 :    
642 :     * R/diagMatrix.R (%*%): rep(*, each = .) in Matrix %*% diagonal.
643 :     * tests/matprod.R: add tests for the bug fixed.
644 :    
645 : bates 1624 2006-10-11 Douglas Bates <bates@stat.wisc.edu>
646 :    
647 :     * src/HBMM.[ch]: remove HarwellBoeing format for writing.
648 :     * src/SOURCES_C.mkf (SOURCES_C): no longer compile iohb.c
649 :    
650 :     2006-10-06 Douglas Bates <bates@stat.wisc.edu>
651 :    
652 : bates 1629 * R/d[gs]CMatrix.R: deprecate the writeHB function. Use writeMM instead.
653 : bates 1624
654 : maechler 1618 2006-10-06 Martin Maechler <maechler@stat.math.ethz.ch>
655 :    
656 :     * DESCRIPTION (Version): 0.9975-3
657 :    
658 :     * R/diagMatrix.R (bdiag): new function constructing block diagonal
659 :     (sparse) matrices.
660 :     * man/bdiag.Rd: docu + examples
661 :    
662 : maechler 1619 * R/Csparse.R (replCmat): calling new Csparse_drop() now.
663 :    
664 : maechler 1618 * src/Csparse.c (Csparse_general_to_symmetric, Csparse_drop): new functions
665 :     * R/lsCMatrix.R: three more coercions to lsC (thanks to the above)
666 :    
667 :     * R/diagMatrix.R (Diagonal): '[<-' method for diag.matrices such
668 :     that result is sparse or diagonal (and not dense).
669 :    
670 :     * man/Subassign-methods.Rd: fix examples
671 :    
672 :     * R/Matrix.R (Matrix): Matrix(0, *) or Matrix(*, sparse=TRUE)
673 :     should always return a sparse (and not sometimes a diagonal) matrix.
674 :    
675 : maechler 1615 2006-10-05 Martin Maechler <maechler@stat.math.ethz.ch>
676 :    
677 :     * R/Matrix.R ([<-): also for value "Matrix" or "matrix"
678 :    
679 : bates 1613 2006-10-04 Douglas Bates <bates@stat.wisc.edu>
680 :    
681 :     * DESCRIPTION (Version): 0.9975-2
682 : maechler 1615
683 : bates 1613 * inst/include/Matrix_stubs.c (M_cholmod_sparse_to_triplet): export more symbols
684 :    
685 : bates 1611 2006-10-02 Douglas Bates <bates@R-project.org>
686 :    
687 :     * tests/dg_Matrix.R: Simplify test taking into account new code.
688 :    
689 : maechler 1599 2006-09-29 Martin Maechler <maechler@stat.math.ethz.ch>
690 :    
691 : maechler 1600 * R/Csparse.R (replCmat): improve for missing i / j in non-simple cases
692 :    
693 : maechler 1599 * R/lsTMatrix.R: new files w/ missing methods
694 :     * R/nsTMatrix.R: " 'for completeness'
695 :    
696 :     * tests/Class+Meth.R: a bit less 'not.ok.classes'
697 :    
698 :     * R/Tsparse.R (t): generalized "t" method from "dgT*" to "Tsparse*"
699 :    
700 :    
701 : bates 1595 2006-09-28 Douglas Bates <bates@R-project.org>
702 :    
703 :     * src/dppMatrix.h: Ensure definition of dspMatrix_validate is
704 :     included.
705 :    
706 :     * src/init.c, inst/include/{Matrix.h,Matrix_stubs.h,cholmod.h}:
707 :     Export C-callable functions used in Zt_create in lme4.
708 :    
709 : maechler 1592 2006-09-28 Martin Maechler <maechler@stat.math.ethz.ch>
710 :    
711 :     * DESCRIPTION (Version): 0.9975-1
712 :    
713 :     * tests/simple.R: less checks fail; using NA, found that our
714 :     kronecker() is not base-compatible with NA's.
715 :    
716 :     * R/dMatrix.R: "Compare" method now implemented for all cases
717 :    
718 :     * R/Auxiliaries.R (indTri): == which([lower/upper].tri( * )) new utility
719 :    
720 :     * man/dtpMatrix-class.Rd: mention length of 'x' slot
721 :    
722 :     * src/dtpMatrix.c (dtpMatrix_validate): fix check
723 :     * src/dspMatrix.c (dspMatrix_validate): ditto
724 :    
725 :     * R/dtTMatrix.R (gt2tT): fix ("l" -> "n")
726 :     including coercion to [nl]tTMatrix.
727 :    
728 :     * R/diagMatrix.R (show): print a header line as for other classes.
729 :    
730 :     2006-09-27 Martin Maechler <maechler@stat.math.ethz.ch>
731 :    
732 :     * src/Makefile.win (SUBDIRS): fix typo
733 :    
734 : maechler 1583 2006-09-19 Martin Maechler <maechler@stat.math.ethz.ch>
735 :    
736 :     * DESCRIPTION (Date): ready to release 0.9975-0 to CRAN
737 :    
738 : bates 1577 2006-09-18 Douglas Bates <bates@stat.wisc.edu>
739 :    
740 :     * R/[CT]sparse.R (crossprod and tcrossprod): Handle the cases for x
741 :     symmetric and y missing in R code using %*% (cholmod_aat doesn't
742 :     accept a symmetric matrix).
743 :     * tests/group-methods.R: Uncomment test of crossprod applied to
744 :     lsCMatrix objects.
745 :    
746 : maechler 1575 2006-09-18 Martin Maechler <maechler@stat.math.ethz.ch>
747 :    
748 :     * R/AllClass.R (symmetricMatrix): add validity method (available
749 :     in C for a long time). Many "n..Matrix": drop (wrong) validity arg.
750 :    
751 :     * src/lgCMatrix.c (lgCMatrix_validate): check 'x' slot (!)
752 :    
753 :     * tests/indexing.Rout.save:
754 :     * tests/indexing.R: additions, mainly for 'lsparse'
755 :    
756 :     * R/diagMatrix.R (Diagonal) & coercion to lgTMatrix: fixes for NA
757 :     case.
758 :    
759 :     * R/Auxiliaries.R (nz.NA): new utility now used in nnzero()
760 :    
761 : maechler 1571 2006-09-16 Martin Maechler <maechler@stat.math.ethz.ch>
762 :    
763 : maechler 1572 * R/sparseMatrix.R (prSpMatrix): print logical NAs "visibly"
764 :     as 'N' (1-letter - Ok?)
765 :    
766 : maechler 1571 * tests/group-methods.R: add test for logical + NAs
767 :    
768 :     * R/dMatrix.R ("Compare"): fix to work with NA's
769 :    
770 :     * R/AllClass.R: "Cholesky" etc now inherit from MatrixFactorization.
771 :    
772 :     * src/lgCMatrix.c (ncsc_to_matrix): renamed from lcsc_to_matrix()
773 :     which is implemented.
774 :    
775 : maechler 1565 2006-09-15 Martin Maechler <maechler@stat.math.ethz.ch>
776 :    
777 : maechler 1571 * src/chm_common.c: coerce logical <-> double instead of
778 :     typecasting; needed for "l" matrix handling in cholmod.
779 : maechler 1565
780 : maechler 1571 * tests/other-pkgs.R (graph): small extension in "graph" checks.
781 :    
782 : maechler 1565 * R/sparseMatrix.R (graphNEL -> Tsparse): method for weight case.
783 :     (Tsp2grNEL): other fixes needed
784 :    
785 : maechler 1548 2006-09-11 Martin Maechler <maechler@stat.math.ethz.ch>
786 :    
787 :     * R/AllClass.R ("nMatrix"): and subclasses for "nonzero pattern"
788 :     Matrices, since "lMatrix", also "lsparseM" can have NA
789 :     * R/ndenseMatrix.R, etc: new source files
790 :     * man/nsparseMatrix-classes.Rd, etc: new help files
791 :     * tests/: adaptions
792 :     * src/chm_common.c (chm_dense_to_SEXP): and others:
793 :     new 'Rkind' argument: "l*" and "d*" both use CHOLMOD_REAL
794 : maechler 1582 * src/Csparse.c, etc: ditto
795 : maechler 1548
796 : bates 1546 2006-09-11 Douglas Bates <bates@R-project.org>
797 :    
798 :     * src/Mutils.[ch],init.c inst/include/*.h: Move the
799 :     alloc_d**Matrix functions to the lme4 package.
800 :    
801 : bates 1543 2006-09-09 Douglas Bates <bates@R-project.org>
802 :    
803 :     * src/dsCMatrix.c (dsCMatrix_Cholesky): igoring LDL = FALSE now
804 : maechler 1544 fixed
805 : bates 1543
806 : maechler 1544 2006-09-09 Martin Maechler <maechler@stat.math.ethz.ch>
807 :    
808 : maechler 1548 * R/lMatrix.R: new
809 :    
810 : maechler 1544 * R/sparseMatrix.R (Tsp2grNEL): do not yet use graph::foo()
811 :    
812 :     * R/dgeMatrix.R: do not define tcrossprod() methods for "matrix"
813 : maechler 1582 * man/tcrossprod.Rd: ditto
814 : maechler 1544
815 : bates 1538 2006-09-08 Douglas Bates <bates@stat.wisc.edu>
816 :    
817 :     * inst/include/Matrix_stubs.c,Matrix.h: Add declarations and stubs
818 :     for exported functions
819 :     * src/Makefile, src/CHOLMOD/Lib/Makefile, src/Metis,CAMD,CCOLAMD:
820 :     Remove partitioning algorithms for sparse matrix reordering. The
821 :     copyright on the Metis code was problematic and the methods were
822 :     rarely used.
823 :     * src/triplet_to_col.[ch],MMHB.[ch]: Remove triplet_to_col. Such
824 :     operations are now done entirely in CHOLMOD code.
825 :    
826 : bates 1517 2006-09-06 Douglas Bates <bates@R-project.org>
827 :    
828 :     * src/Mutils.h: Remove functions that are no longer used.
829 :    
830 : bates 1507 2006-09-04 Douglas Bates <bates@R-project.org>
831 :    
832 :     * src/dtCMatrix.c (dtCMatrix_validate): rename functions.
833 :     * src/DEPS.mkf: update
834 :    
835 : maechler 1481 2006-09-02 Martin Maechler <maechler@stat.math.ethz.ch>
836 :    
837 :     * created branches/Matrix-for-R-2.3.x; on trunk: do
838 :     * DESCRIPTION (Version): 0.9975-0
839 :     (Depends): R (>= 2.4.0)
840 :    
841 : bates 1475 2006-09-01 Douglas Bates <bates@R-project.org>
842 :    
843 :     * R/sparseMatrix.R: Added direct method to CsparseMatrix from graphNEL
844 :    
845 : maechler 1472 2006-09-01 Martin Maechler <maechler@stat.math.ethz.ch>
846 :    
847 :     * R/sparseMatrix.R: add coercion from "ANY" to "sparseMatrix"
848 :     * R/denseMatrix.R: add coercion from "ANY" to "denseMatrix"
849 :    
850 :     * R/Matrix.R ([): use nargs() to disambiguate M[i] and M[i,]
851 :    
852 :     2006-08-31 Martin Maechler <maechler@stat.math.ethz.ch>
853 :    
854 :     * R/sparseMatrix.R (Arith): moved Arith group method one-level up
855 :     from "dsparse" to "sparse" and now go via "Csparse" instead of "dgC"
856 : maechler 1582 * R/dsparseMatrix.R: ditto
857 :     * R/Csparse.R: ditto
858 : maechler 1472
859 :     2006-08-31 Martin Maechler <maechler@stat.math.ethz.ch>
860 :    
861 :     * R/dMatrix.R (Compare): improve availability of "<", etc
862 :     * R/Auxiliaries.R (asTuniq): new; also make use of R 2.4.x print(*,max)
863 :    
864 : maechler 1467 2006-08-30 Martin Maechler <maechler@stat.math.ethz.ch>
865 :    
866 :     * R/dgCMatrix.R: aargh: "Arith(<dgC>, numeric)" was wrong because
867 :     of a 0-index which was used as 1-index (..hmm)
868 :    
869 :     * R/sparseMatrix.R (prSpMatrix): fix printing an all-0 sparse Matrix
870 :    
871 :     * R/Auxiliaries.R (all0, is0): for 0-testing in presence of NA's
872 :     * R/Auxiliaries.R (isTriMat): use all0() for 0-testing.
873 : maechler 1582 (.is.diagonal): ditto
874 : maechler 1467
875 :     * R/lgTMatrix.R: as("matrix", "lgTMatrix"): warn about NA's
876 :    
877 :     * R/Matrix.R (Matrix): also work for NA data
878 :    
879 : maechler 1455 2006-08-28 Martin Maechler <maechler@stat.math.ethz.ch>
880 :    
881 :     * R/Matrix.R (Matrix): + 'forceCheck' argument; dimnames setting
882 :     in all cases.
883 :    
884 : bates 1453 2006-08-27 Douglas Bates <bates@R-project.org>
885 :    
886 :     * src/dense.[ch],init.c, R/ddenseMatrix.R, man/band.Rd
887 :     (ddense_band): Added triu, tril and band for ddenseMatrix objects.
888 :    
889 : maechler 1447 2006-08-25 Martin Maechler <maechler@stat.math.ethz.ch>
890 :    
891 :     * src/Mutils.c (dup_mMatrix_as_dgeMatrix): added all subclasses of
892 :     subclasses of "ddenseMatrix"
893 :     * src/init.c et al: outcomment dtrM*_as_dge* and dsyM*_as_dge*_
894 :     * R/ddenseMatrix.R et al: setAs("ddenseMatrix", "dgeMatrix", ..)
895 :     instead of half dozen specialized ones.
896 :    
897 : bates 1445 2006-08-25 Douglas Bates <bates@R-project.org>
898 :    
899 :     * R/lmer.R (qqmath method): Bug fix provided by Emmanuel Tillard
900 :     <tillard@cirad.fr> - ordering standard errors to match effects.
901 :    
902 : bates 1439 2006-08-24 Douglas Bates <bates@R-project.org>
903 : bates 1431
904 : bates 1439 * src/lsCMatrix.c (lsCMatrix_trans): Remove lsCMatrix_chol based
905 :     on R_ldl.
906 :     * R/lCholCMatrix.R,
907 :     src/[dl]CholCMatrix.[ch],R_ldl.[ch],Metis_utils.[ch]: removed
908 :     * src/dsCMatrix.c (dsCMatrix_to_dgTMatrix): use CHOLMOD
909 :     * many files in ./R and ./src: Use more general version of
910 :     dup_mMatrix_as_dgeMatrix to simplify method definitions.
911 : bates 1442 * src/Mutils.c (dup_mMatrix_as_dgeMatrix): Add ddiMatrix,
912 :     dtpMatrix, dspMatrix and dppMatrix conversions.
913 :    
914 : maechler 1447
915 : bates 1439 2006-08-23 Douglas Bates <bates@R-project.org>
916 :    
917 :     * R/AllClass.R,lCholCMatrix.R,src/SOURCES_C.mkf,init.c,NAMESPACE:
918 :     Remove classes lCholCMatrix and dCholCMatrix based on R_ldl code.
919 : bates 1431 * src/dgeMatrix.c: Ensure 'factors' slot exists in result of
920 :     dgeMatrix_crossprod (may need to do this in other places).
921 :     * R/AllGeneric.R,dsCMatrix.R, src/dscMatrix.[ch]: Add Cholesky
922 :     generic and method for dsCMatrix. Use CHOLMOD for chol().
923 :    
924 : bates 1414 2006-08-22 Douglas Bates <bates@R-project.org>
925 :    
926 :     * src/Mutils.c (dup_mMatrix_as_dgeMatrix): updated for general
927 :     types of classed Matrices, matrices or numeric or logical vectors.
928 : bates 1423 * src/init.c: register dup_mMatrix_as_dgeMatrix for coercions.
929 :     * src/chm_common.c,Mutils.h (as_cholmod_factor): Move check_class
930 :     to Mutils.h (as an inline) and change name to Matrix_check_class;
931 :     fixes in as_cholmod_factor and chm_factor_to_SEXP.
932 :     * src/dsCMatrix.[ch]: Use CHOLMOD for dsCMatrix_chol and
933 :     dsCMatrix_matrix_solve. Comment out vestigial functions.
934 :     * src/Csparse.c: use diag_P and uplo_P macros.
935 : maechler 1447
936 : bates 1405 2006-08-21 Douglas Bates <bates@R-project.org>
937 :    
938 :     * src/lmer.c (internal_mer_RZXinv): Fix memory leak caught by
939 : maechler 1447 valgrind.
940 : bates 1411 * tests/matprod.R: Add tests to verify that 'solve' and '%*%' are
941 :     inverses.
942 :     * src/sparseQR.c (sparseQR_validate): add new validation test, fix
943 :     -Wall warnings.
944 :     * src/dppMatrix.c,dtrMatrix.c,dgCMatrix.c,dgeMatrix.c,dspMatrix.c:
945 :     Use dup_mMatrix_as_dgeMatrix.
946 : maechler 1447
947 : bates 1403 2006-08-20 Douglas Bates <bates@R-project.org>
948 :    
949 :     * src/sparseQR.c: Fix thinko in sparseQR_resid_fitted.
950 :     * tests/sparseQR.R: Added
951 :     * man/sparseQR-class.Rd: Document methods for qr.* generics
952 :     * R/sparseQR.R: Return correct # of coefs; fix cut-and-paste errors
953 :    
954 : bates 1398 2006-08-19 Douglas Bates <bates@R-project.org>
955 :    
956 :     * NAMESPACE, R/sparseQR.R, src/init.c,sparseQR.[ch],SOURCES_C.mkf:
957 :     Added methods for sparseQR for qr.qy, qr.qty, qr.coef, qr.resid
958 :     and qr.fitted.
959 :     * src/Mutils.[ch]: Added dup_mMatrix_as_dgeMatrix utility
960 :     * src/dgCMatrix.c: Check for ordering before storing q in dgCMatrix_QR
961 :    
962 : maechler 1389 2006-08-18 Martin Maechler <maechler@stat.math.ethz.ch>
963 :    
964 :     * R/AllGeneric.R: add "qr" and "chol" generics; via 'trick' since
965 :     the base version has no "..." argument.
966 :    
967 :     * R/sparseMatrix.R (prSpMatrix): fix the triangular unit diagonal case.
968 :    
969 :     * R/Matrix.R: define and
970 :     * NAMESPACE: export as.numeric() and as.logical() methods.
971 :     Let's hope these do not badly slow down something...
972 :     Finally export the zapsmall() method.
973 :    
974 : bates 1388 2006-08-17 Douglas Bates <bates@R-project.org>
975 :    
976 :     * src/dgCMatrix.[ch] (dgCMatrix_matrix_solve), src/init.c,
977 :     R/dgCMatrix.R: solve methods for dgCMatrix and dense RHS.
978 :     * src/dtCMatrix.c :Remove code that is no longer used
979 :     * R/dtCMatrix.R: Use C code for diagU2N in CsparseMatrix classes
980 :    
981 : bates 1370 2006-08-14 Douglas Bates <bates@R-project.org>
982 :    
983 : bates 1373 * src/Csparse.[ch],init.c (Csparse_to_logical): Added utilities
984 :     Csparse_to_logical and Csparse_symmetric_to_general.
985 :     * R/dgCMatrix.R,dsCMatrix.R,Csparse.R : Consolidate general
986 : maechler 1389 coercion methods between CsparseMatrix and TsparseMatrix.
987 : bates 1373
988 :     2006-08-14 Douglas Bates <bates@R-project.org>
989 :    
990 : bates 1370 * R/dtCMatrix.R,dgCMatrix.R,Csparse.R src/init.c,dgCMatrix.[ch],
991 :     Csparse.[ch],chm_common.c,dense.c : Use CHOLMOD code and methods
992 :     for CsparseMatrix, TsparseMatrix, denseMatrix or matrix when
993 :     possible.
994 :    
995 : bates 1368 2006-08-12 Douglas Bates <bates@R-project.org>
996 :    
997 :     * src/chm_common.[ch],Csparse.[ch],Tsparse.[ch],CHMfactor.c,dtTMatrix.c,
998 :     dgTMatrix.c,dgCMatrix.c,dsCMatrix.c,dtTMatrix.c, R/dsTMatrix.R,
999 :     Tsparse.R,Csparse.R,dgTMatrix.R,dsCMatrix.R,lsCMatrix.R:
1000 :     generalize conversions between TsparseMatrix, CsparseMatrix,
1001 :     denseMatrix and matrix. Preserve triangularity property and
1002 :     propagate Dimnames in the easy cases.
1003 :    
1004 : bates 1365 2006-08-10 Douglas Bates <bates@R-project.org>
1005 :    
1006 :     * src/lmer.c: adjust checks in glmer_init for S4SXP
1007 :     * tests/validObj.R: check of all(eq) should be all(eq@x) - worked
1008 :     before S4SXP but for the wrong reasons.
1009 :    
1010 : bates 1354 2006-08-08 Douglas Bates <bates@R-project.org>
1011 :    
1012 : bates 1360 * src/Csparse.c (Csparse_crossprod): tcrossprod result has stype = -1.
1013 :     Later modified to return the upper triangle only.
1014 :     * R/dgTMatrix.R: Remove vestigial crossprod and tcrossprod methods.
1015 : maechler 1389
1016 : bates 1352 2006-08-07 Douglas Bates <bates@R-project.org>
1017 :    
1018 :     * src/Csparse.c (Csparse_crossprod): Set stype on result to avoid
1019 :     R-level conversion to a sparse symmetric class.
1020 :     * R/Tsparse.R,R/Csparse.R (crossprod and tcrossprod methods):
1021 :     Remove conversion to sparse symmetric classes (now done in C code).
1022 :    
1023 : maechler 1349 2006-08-07 Martin Maechler <maechler@stat.math.ethz.ch>
1024 :    
1025 : maechler 1351 * R/dgCMatrix.R: disable old crossprod and tcrossprod methods
1026 :     * man/band.Rd: adapt the \dontshow{} unit test.
1027 :    
1028 :     2006-08-07 Martin Maechler <maechler@stat.math.ethz.ch>
1029 :    
1030 : maechler 1349 * DESCRIPTION (Version): 0.995-14 for CRAN
1031 :    
1032 :     * tests/other-pkgs.R: oops: library(Matrix) outside *if* !
1033 :    
1034 :     * R/sparseMatrix.R (Tsp2grNEL): fixed Tsparse -> graph coercion
1035 :     * tests/other-pkgs.R: more checks, sparseMatrix -> graph
1036 :    
1037 :     * R/Auxiliaries.R (as_Tsparse, as_Rsparse): new
1038 :     * R/Tsparse.R (tril, triu, band): methods
1039 : bates 1352 * R/dgRMatrix.R (tril, ...): ditto
1040 :     * man/band.Rd: ditto
1041 : maechler 1349
1042 :     2006-08-04 Martin Maechler <maechler@stat.math.ethz.ch>
1043 :    
1044 :     * R/Matrix.R (head, tail): directly use utils:::head.matrix
1045 :     to be up-to-date automatically.
1046 :    
1047 : maechler 1346 2006-08-03 Martin Maechler <maechler@stat.math.ethz.ch>
1048 :    
1049 :     * DESCRIPTION (Version): 0.995-13 to be released to CRAN
1050 :    
1051 :     * DESCRIPTION (Lazydata): no, instead of 'yes' because it fails for:
1052 :     * data/CAex.R, inst/external/CAex_slots.rda: replacing data/CAex.rda
1053 :     * data/KNex.R, inst/external/KNex_slots.rda: replacing data/KNex.rda
1054 :     such that the S4 objects are always created by the current version
1055 :     of R and 'Matrix' class definitions.
1056 :    
1057 : bates 1342 2006-08-01 Douglas Bates <bates@R-project.org>
1058 :    
1059 :     * R/lmer.R (LMEoptimize method), tests/lmer.R,
1060 : maechler 1346 inst/external/test3comp.rda: Added warnings for convergence on
1061 : bates 1342 boundary and test cases.
1062 :    
1063 :     * src/lmer.c (mer_postVar): Modified to return the variances that
1064 :     are marginal to the fixed effects, not conditional on them (which
1065 :     is what the bVar slot contents represent).
1066 :    
1067 : bates 1338 2006-07-31 Douglas Bates <bates@R-project.org>
1068 :    
1069 :     * NAMESPACE, src/lmer.c, R/lmer.R (hatTrace): Add the hatTrace
1070 :     function which calls the C function mer_hat_trace2.
1071 : maechler 1346
1072 : bates 1342 * man/ranef.Rd: Include description of "postVar" argument and
1073 :     producing a caterpillar plot.
1074 : bates 1338
1075 : maechler 1335 2006-07-31 Martin Maechler <maechler@stat.math.ethz.ch>
1076 :    
1077 :     * NAMESPACE: change "correlation" to "corMatrix"
1078 :     * R/AllClass.R: to avoid clash with S3 class in 'nlme'.
1079 : bates 1352 * R/dpoMatrix.R: ditto
1080 :     * R/lmer.R: ditto
1081 : maechler 1335
1082 : bates 1338 2006-07-28 Douglas Bates <bates@R-project.org>
1083 :    
1084 :     * src/lmer.c (internal_mer_RZXinv): Split the calculation of the
1085 :     RZXinv slot's contents into a separate internal function that can
1086 :     be used in mer_hat_trace.
1087 :    
1088 : maechler 1331 2006-07-22 Martin Maechler <maechler@stat.math.ethz.ch>
1089 :    
1090 :     * R/Matrix.R: Coercions "Matrix" -> (sparse|dense)Matrix
1091 :     via new smart
1092 :     * R/Auxiliaries.R (as_Csparse, as_dense, .M.shapse): new
1093 :     utility functions.
1094 :    
1095 :    
1096 : maechler 1330 2006-07-21 Martin Maechler <maechler@stat.math.ethz.ch>
1097 :    
1098 : maechler 1331 * R/Csparse.R (tril, triu, band): do return *triangular* classed
1099 :     matrices when appropriate; band() even symmetric ones.
1100 :     (replCmat): extend to potentially all "CsparseMatrix"
1101 :     * R/Tsparse.R (replTmat): extend to all "TsparseMatrix"; hence
1102 :     allow subassignment for special sparse matrices.
1103 :    
1104 :     * R/Auxiliaries.R (as_geClass): factor out the .M.kind() functionality
1105 :    
1106 : maechler 1330 * src/lmer.c (mer_MCMCsamp, glmer_MCMCsamp): new 'verbose'
1107 :     argument; in glmer_*(): print only if(verbose).
1108 :    
1109 :     speed-optimize a few places by moving REAL(.) out of loops.
1110 :    
1111 :     * src/lmer.h, src/init.h, R/lmer.R: related to above.
1112 :    
1113 : maechler 1329 2006-07-20 Martin Maechler <maechler@stat.math.ethz.ch>
1114 :    
1115 :     * R/Matrix.R("["): disable ("Matrix", i = "logical", j = "missing"),
1116 :     since that wrongly triggers also for M[ logi , ]
1117 :    
1118 :     * R/denseMatrix.R: "[" methods now also work e.g. when indexing
1119 :     a symmetric matrix that results in a non-symmetric one.
1120 :     * R/Auxiliaries.R (as_geClass): new function used in "[" above.
1121 :    
1122 :     * R/dMatrix.R: make round(M) work as round(M, 0)
1123 :    
1124 :     * R/dgTMatrix.R (image): coordinate system and axis now use
1125 :     1-based indices, not 0-based ones.
1126 :    
1127 :     * R/Tsparse.R (.ind.prep for "["): get rid of max(<empty>) warning.
1128 :     * tests/indexing.R: test it.
1129 :    
1130 :     * NAMESPACE: export isSymmetric(); has been a generic in "base" for a while;
1131 :     * man/isSymmetric-methods.Rd: and document it.
1132 :    
1133 :     * R/SparseM-conv.R: added coercion methods for some 'SparseM' matrices.
1134 :     * man/SparseM-conv.Rd: docu them
1135 :    
1136 :     * tests/other-pkgs.R: renamed from tests/graph.R and add example
1137 :     for 'SparseM' conversions
1138 :    
1139 :     2006-07-17 Douglas Bates <Douglas.Bates@R-project.org>
1140 :    
1141 :     * R/Matrix.R (head): added head() and tail() methods.
1142 :    
1143 :     2006-07-17 Martin Maechler <maechler@stat.math.ethz.ch>
1144 :    
1145 :     * DESCRIPTION (Version): 0.995-12 released to CRAN
1146 :    
1147 : maechler 1319 2006-07-15 Martin Maechler <maechler@stat.math.ethz.ch>
1148 :    
1149 :     * tests/simple.R: add check for correct dsT -> dgT coercion;
1150 :     add check for correct printing of symmetric sparse matrices.
1151 :    
1152 :     * R/Auxiliaries.R (non0ind): return *all* non-0 entry indices also
1153 :     for sparse symmetric matrices.
1154 :    
1155 :     * src/dsTMatrix.c (dsTMatrix_as_dgTMatrix): do not copy the
1156 :     diagonal twice.
1157 :    
1158 : bates 1316 2006-07-11 Douglas Bates <Douglas.Bates@R-project.org>
1159 :    
1160 :     * src/dsTMatrix.c (dsTMatrix_as_dgTMatrix): Fix a case of INTEGER
1161 : maechler 1319 being applied to the x slot (detected by Brian Ripley).
1162 : bates 1316
1163 : maechler 1315 2006-07-10 Martin Maechler <maechler@stat.math.ethz.ch>
1164 :    
1165 :     * src/dgCMatrix.c (dgCMatrix_validate): 'p' slot must have correct length.
1166 :    
1167 :     * R/Auxiliaries.R (isTriC): fix buglet (we were 1-based!)
1168 :    
1169 :     2006-07-08 Martin Maechler <maechler@stat.math.ethz.ch>
1170 :    
1171 :     * src/lgCMatrix.c (lgCMatrix_diag): new function
1172 :     * R/lgCMatrix.R (diag): for new method
1173 :    
1174 :     * R/AllClass.R (TsparseMatrix): do use Tsparse_validate
1175 :     ==> construction of illegal "*gTMatrix" via new() should
1176 :     now be much less easy:
1177 :     * tests/Class+Meth.R: assertError() for some illegal "dgT*"
1178 :    
1179 :     * R/Matrix.R (Matrix): Matrix(0, nrow,ncol) now "goes sparse"
1180 :     directly.
1181 :     * man/Matrix.Rd: documents it.
1182 :    
1183 : bates 1311 2006-07-06 Douglas Bates <bates@R-project.org>
1184 :    
1185 :     * src/pedigree.c (pedigree_inbreeding): Correction in
1186 :     initialization. This function is not currently being used and is
1187 :     not fully tested.
1188 :    
1189 : bates 1312 * NAMESPACE, R/{AllClass.R,lmer.R}, src/{init.c,lmer.c}:
1190 :     Introduced the glmer class. Added code for mcmcmsamp on glmer
1191 :     objects. Modified validity check on pedigree objects to account
1192 :     for nonparallel patterns of missingness of parents.
1193 : bates 1311
1194 : bates 1313 * man/{lmer-class.Rd,mcmcsamp.Rd}: Update documentation for glmer
1195 :     class.
1196 : maechler 1315
1197 :     2006-07-01 Martin Maechler <maechler@stat.math.ethz.ch>
1198 :    
1199 :     * R/pMatrix.R: coercion pMatrix -> Tsparse
1200 :    
1201 : bates 1300 2006-06-12 Douglas Bates <bates@R-project.org>
1202 :    
1203 : maechler 1319 * DESCRIPTION (Version): 0.995-11 released to CRAN
1204 :    
1205 : bates 1300 * R/lmer.R (mcmcsamp method): Corrected arrangments of names on
1206 :     the output from mcmcsamp.
1207 :    
1208 : bates 1298 2006-06-10 Douglas Bates <bates@R-project.org>
1209 :    
1210 : bates 1300 * R/lmer.R (simulestimate): added C code for calculating the trace
1211 :     of the hat matrix.
1212 : bates 1298
1213 : maechler 1295 2006-06-09 Martin Maechler <maechler@stat.math.ethz.ch>
1214 :    
1215 :     * R/diagMatrix.R (setAs): define coercion methods to sparse matrix
1216 :     classes.
1217 : maechler 1315 * R/sparseMatrix.R etc: multiplication of diagonal and sparse
1218 : maechler 1295
1219 : maechler 1290 2006-06-08 Martin Maechler <maechler@stat.math.ethz.ch>
1220 :    
1221 :     * R/dgTMatrix.R (colSums): etc. All four of
1222 :     colSums(), rowSums(), colMeans(), rowMeans() now should work for
1223 :     all "Matrices".
1224 :    
1225 : bates 1288 2006-06-01 Douglas Bates <bates@stat.wisc.edu>
1226 :    
1227 :     * R/lmer.R (panel.ci): Add a reference line at zero and a
1228 :     background grid to the qqmath plot of ranef.lmer.
1229 :    
1230 : bates 1287 2006-05-30 Douglas Bates <bates@stat.wisc.edu>
1231 : bates 1284
1232 : bates 1287 * R/lmer.R (expandSlash): Functions (non-exported) to allow nested
1233 :     grouping factors to be specified in the formula as (1|foo/bar).
1234 :    
1235 :     2006-05-27 Douglas Bates <bates@stat.wisc.edu>
1236 :    
1237 : bates 1284 * R/lmer.R (findbars and others): Change check of is.numeric to
1238 :     !is.language to resolve the bug reported by Jacob Wegelin.
1239 :    
1240 :     * src/pedigree.c (pedigree_inbreeding): Initial implementation of
1241 :     code to evaluate inbreeding coefficients without calculating T,
1242 :     based on code in Sargolzaei and Iwaisaki's paper.
1243 :    
1244 : bates 1283 2006-05-27 Douglas Bates <bates@stat.wisc.edu>
1245 :    
1246 :     * R/{lmer.R,AllGeneric.R}, src/{init.c,lmer.[ch]}: Added local
1247 :     generic and mer methods for isNested and denomDF. This denomDF was
1248 :     an attempt to emulate that in lme but I don't think that makes
1249 :     sense. Use the trace of the hat matrix instead.
1250 :    
1251 : maechler 1271 2006-05-17 Martin Maechler <maechler@stat.math.ethz.ch>
1252 :    
1253 :     * R/sparseMatrix.R: Matrix <-> graph methods: can no longer use
1254 :     the C code depending on a slot structure that's no longer valid.
1255 : bates 1352 * src/dgTMatrix.c: ditto (also: src/init.c src/dgTMatrix.h)
1256 : maechler 1271
1257 :    
1258 : bates 1268 2006-05-17 Douglas Bates <bates@stat.wisc.edu>
1259 :    
1260 :     * R/{AllGeneric.R,Csparse.R},man/band.Rd,NAMESPACE: changed name
1261 :     of lowerTriMatrix generic and methods to tril (also upper to triu)
1262 :     and added a general band extractor.
1263 :    
1264 : bates 1267 2006-05-16 Douglas Bates <bates@stat.wisc.edu>
1265 :    
1266 :     * R/pedigree.R (pedigree): Replace sire and dam values outside the
1267 :     allowable range with NAs. Added a corresponding check in the
1268 :     validity check for the pedigree class.
1269 :    
1270 :     * R/[CT]sparse.R ([t]crossprod): The result of single-argument
1271 :     crossprod methods now inherits from symmetricMatrix.
1272 :    
1273 : bates 1265 2006-05-15 Douglas Bates <bates@stat.wisc.edu>
1274 :    
1275 :     * R/AllGeneric.R (lowerTriMatrix): Added (but did not export)
1276 :     generics lowerTriMatrix and upperTriMatrix along with methods for
1277 :     the Csparse virtual class. Also added a C function Csparse_band
1278 :     that implements these methods by calling cholmod_band.
1279 :    
1280 : maechler 1264 2006-05-15 Martin Maechler <maechler@stat.math.ethz.ch>
1281 :    
1282 :     * R/Tsparse.R ("["): column or row subsetting; @Dimnames[k] got
1283 :     erased when it was NULL. This led to invalid subselections!
1284 :    
1285 : bates 1259 2006-04-25 Douglas Bates <bates@stat.wisc.edu>
1286 :    
1287 :     * R/dtCMatrix.R: avoid coercion of dtCMatrix object to dgCMatrix
1288 :     in method for "t" so as not to lose the unit diagonal property.
1289 :    
1290 : bates 1257 2006-04-19 Douglas Bates <bates@stat.wisc.edu>
1291 :    
1292 :     * R/lmer.R, R/AllGeneric.R, NAMESPACE: Remove the postVar generic
1293 :     and methods. This is now an option to the ranef method for the
1294 :     mer class.
1295 :    
1296 :     * src/cs_utils.c: Ensure that the nz component is -1 for a
1297 :     compressed column-oriented matrix. Minor formatting cleanup.
1298 :    
1299 :     * man/lmer-class.Rd: Document the qqmath method for ranef.lmer
1300 :     objects.
1301 :    
1302 : maechler 1253 2006-04-19 Martin Maechler <maechler@stat.math.ethz.ch>
1303 :    
1304 :     * R/Auxiliaries.R (diagU2N): new for the solve() methods in
1305 :     * R/dtCMatrix.R: where dgC -> dgT coercion now preserves diag = "U".
1306 :    
1307 : bates 1251 2006-04-15 Douglas Bates <bates@stat.wisc.edu>
1308 :    
1309 :     * src/cs.[ch],src/cs_utils.[ch] : Added Tim Davis' CSparse library
1310 :     in cs.[ch] and utilities to interface to that code in cs_utils.[ch].
1311 :    
1312 :     * R/dtCMatrix.R, src/dtCMatrix.[ch] : CSparse-based solve methods
1313 :     for the dtCMatrix class.
1314 : maechler 1253
1315 : bates 1247 2006-04-12 Douglas Bates <bates@stat.wisc.edu>
1316 :    
1317 :     * R/pedigree.R, R/AllClass.R, NAMESPACE: added a pedigree class
1318 :     and methods for it.
1319 :    
1320 : maechler 1245 2006-04-12 Martin Maechler <maechler@stat.math.ethz.ch>
1321 :    
1322 :     * R/dgCMatrix.R: add storage.mode(.) <- "double" for "matrix"
1323 :     arguments, such that M %*% 1:6 now works
1324 :     * Tests/matprod.R: test the above
1325 :    
1326 : bates 1244 2006-04-03 Douglas Bates <bates@stat.wisc.edu>
1327 : bates 1243
1328 :     * R/lmer.R (qqmath,ranef.lmer-method): added a qqmath method for
1329 :     the ranef.lmer class.
1330 :    
1331 :     * R/AllClass.R, NAMESPACE, R/lmer.R: Added a postVar generic and
1332 :     methods to extract the posterior variances from the bVar slot.
1333 :    
1334 : maechler 1238 2006-03-30 Martin Maechler <maechler@stat.math.ethz.ch>
1335 :    
1336 :     * R/dtCMatrix.R: allow coercion from dgC* to triangular (dtC*)
1337 :     * R/dsCMatrix.R: and symmetric (dsC*) 'Csparse' matrices.
1338 :    
1339 :     * R/Tsparse.R: Tsparse* -> Csparse* coercion now works and is tested in
1340 :     * tests/simple: (extended)
1341 :    
1342 :     * R/sparseMatrix.R (isTriangular): now using much improved
1343 :     * R/Auxiliaries.R (isTriC): new triangularity check for *CMatrix
1344 :    
1345 : bates 1236 2006-03-23 Douglas Bates <bates@stat.wisc.edu>
1346 :    
1347 :     * src/dsyMatrix.c (dsyMatrix_as_dspMatrix): Propagate DimNames
1348 :     (problem report from Franklin Parlamis). This should be done
1349 : maechler 1238 generally.
1350 : bates 1236
1351 : bates 1234 2006-03-21 Douglas Bates <bates@stat.wisc.edu>
1352 :    
1353 :     * R/AllClass.R,lmer.R: Change the name of the lmer.ranef class to
1354 :     ranef.lmer (like summary.lmer). Add the coef.lmer class and
1355 :     update the plot methods.
1356 :    
1357 : bates 1232 2006-03-20 Douglas Bates <bates@stat.wisc.edu>
1358 :    
1359 :     * R/lmer.R (resid and ranef methods): Added methods for the
1360 :     "residuals" and "resid" generic but only for linear mixed model
1361 :     fits. Changed the ranef method to return a list of data frames so
1362 :     that the plot methods now work.
1363 :    
1364 : bates 1230 2006-03-16 Douglas Bates <bates@bates2>
1365 :    
1366 :     * src/dpoMatrix.c (dpoMatrix_chol): Require n > 0 in call to
1367 :     dpotrf - otherwise the BLAS on Mac OS X complains and quits.
1368 :    
1369 :     * DESCRIPTION (Date): New release
1370 :    
1371 : maechler 1228 2006-03-15 Martin Maechler <maechler@stat.math.ethz.ch>
1372 :    
1373 :     * DESCRIPTION (Version): 0.995-6 -- to be released to CRAN
1374 :    
1375 :     * data/KNex.rda: replacing 'mm' and 'y' by KNex <- list(mm=mm, y=y)
1376 :     * man/KNex.Rd: and other help files
1377 :     * tests/*.R: several ones needed adaption
1378 : bates 1352 * inst/doc/Comparisons.Rnw: ditto
1379 : maechler 1228
1380 : maechler 1226 2006-03-11 Martin Maechler <maechler@stat.math.ethz.ch>
1381 :    
1382 :     * R/dgCMatrix.R (replCmat): "[<-" methods for dgCMatrix
1383 :    
1384 :     * tests/indexing.R: tests for new [<- methods for sparse matrices.
1385 :    
1386 :     2006-03-10 Martin Maechler <maechler@stat.math.ethz.ch>
1387 :    
1388 :     * R/dgTMatrix.R (replTmat): "[<-" methods for dgTMatrix
1389 :    
1390 :     * R/Tsparse.R (.ind.prep): fix out-of-range indexing
1391 :    
1392 :     2006-03-08 Martin Maechler <maechler@stat.math.ethz.ch>
1393 :    
1394 :     * R/dMatrix.R: enable things like M [ M < 10 ]
1395 :     * R/dgeMatrix.R: implement it
1396 :    
1397 : maechler 1222 2006-03-06 Martin Maechler <maechler@stat.math.ethz.ch>
1398 :    
1399 :     * R/AllClass.R: define "summary.mer" and "*.lmer"
1400 :     * R/lmer.R (summary): summary(<mer>) computes & returns the above;
1401 :     * R/lmer.R (show): now works with summary()
1402 :    
1403 :     2006-03-04 Martin Maechler <maechler@stat.math.ethz.ch>
1404 :    
1405 :     * R/dgCMatrix.R: finally direct "Arith" dgC o dgC
1406 :     * R/Auxiliaries.R (WhichintersectInd): and other utilities to
1407 :     support the above
1408 :    
1409 : bates 1213 2006-02-07 Douglas Bates <bates@stat.wisc.edu>
1410 :    
1411 :     * R/lmer.R (lmer): fix initial values of offset and weights for glm.fit.
1412 :     Use glmFit$prior.weights for weights in a glmm.
1413 :     Allow an option usePQL = FALSE to skip the PQL steps for the
1414 :     Laplace method (and, in time, the AGQ method).
1415 :    
1416 :     * src/lmer.c (mer_factor): Move downdating and factoring of XtX
1417 :     into a separate function internal_mer_Xfactor to be able to call
1418 :     it from internal_bhat.
1419 :    
1420 : maechler 1200 2006-01-23 Martin Maechler <maechler@stat.math.ethz.ch>
1421 :    
1422 :     * tests/Class+Meth.R (tstMatrixClass): function for much better
1423 :     testing; now again of all actual classes.
1424 :    
1425 :     * src/Mutils.c (MAKE_TRIANGULAR_BODY, MAKE_SYMMETRIC_BODY):
1426 :     use macros and define make_d_matrix_* and make_i_matrix_*
1427 :     where _i_ is for the ldense routines:
1428 :    
1429 :     * src/ldense.c (ltrMatrix_as_lgeMatrix): provide functions
1430 :     * src/ldense.c (lsyMatrix_as_lgeMatrix):
1431 :    
1432 :     * R/ldenseMatrix.R: use the above in setAs(*,"lgeMatrix")
1433 :    
1434 :    
1435 : maechler 1174 2006-01-16 Martin Maechler <maechler@stat.math.ethz.ch>
1436 :    
1437 :     * R/Matrix.R (Matrix): has become much "smarter" now auto-producing
1438 :     many different kinds of matrices.
1439 :     * R/*.R: quite a few new methods were needed for R CMD check with
1440 :     new Matrix(). Very good for users playing around.
1441 :    
1442 :    
1443 : maechler 1165 2006-01-15 Martin Maechler <maechler@stat.math.ethz.ch>
1444 :    
1445 :     * src/dgeMatrix.c (dMatrix_validate): new
1446 :     * src/Mutils.c (dense_nonpacked_validate): new
1447 :    
1448 :     * src/dtrMatrix.c (dtrMatrix_validate): improved/fixed
1449 :    
1450 :    
1451 :     2006-01-14 Douglas Bates <bates@stat.wisc.edu>
1452 :    
1453 :     * R/AllClass.R (compMatrix), (generalMatrix): new virtual classes
1454 :    
1455 : bates 1123 2006-01-07 Douglas Bates <bates@stat.wisc.edu>
1456 : bates 1119
1457 : maechler 1127 * DESCRIPTION (Version): 0.99-6 released to CRAN
1458 :    
1459 : bates 1119 * src/dgBCMatrix.c (cscb_trcbsm): Fix due to Peter Dalgaard for
1460 :     segfault in cases with multiple non-nested grouping factors.
1461 :    
1462 : maechler 1109 2006-01-03 Martin Maechler <maechler@stat.math.ethz.ch>
1463 :    
1464 :     * DESCRIPTION (Version): 0.99-4 to be released to CRAN
1465 :     (Depends): also on 'utils'
1466 :    
1467 :     * R/AllClass.R (diagonalMatrix): new class with "ddi*" and "ldi*"
1468 :     * R/diagMatrix.R (Diagonal): constructor and methods for
1469 :     diagonal matrices
1470 :    
1471 :     * R/ltTMatrix.R: new "minimal methods"
1472 :    
1473 : maechler 1091 2005-12-12 Martin Maechler <maechler@stat.math.ethz.ch>
1474 :    
1475 :     * R/AllGeneric.R (tcrossprod): 2-argument version; here, and for
1476 :     all methods (and help files).
1477 :    
1478 : maechler 1084 2005-12-09 Martin Maechler <maechler@stat.math.ethz.ch>
1479 :    
1480 :     * R/Auxiliaries.R (dimNamesCheck): fixed thinko -> bug
1481 :     for case (dimn. op no_dimn.)
1482 :    
1483 :     2005-11-14 Douglas Bates <bates@stat.wisc.edu>
1484 :    
1485 : maechler 1174 * DESCRIPTION (Version): 0.99-2 released to CRAN
1486 : maechler 1084
1487 : bates 988 2005-10-21 Douglas Bates <bates@stat.wisc.edu>
1488 :    
1489 :     * R/lmer.R (simulate method): Fixed a drop=FALSE problem reported
1490 :     by Julian Faraway.
1491 :    
1492 : maechler 976 2005-10-06 Martin Maechler <maechler@stat.math.ethz.ch>
1493 :    
1494 :     * R/Auxiliaries.R (try_as): new utility
1495 :     * R/sparseMatrix.R: use try_as() in coercion to original class
1496 :    
1497 : maechler 956 2005-09-30 Martin Maechler <maechler@stat.math.ethz.ch>
1498 :    
1499 :     * src/dgCMatrix.c (double_to_csc): and dgeMatrix_to_csc()
1500 :    
1501 :     2005-09-29 Martin Maechler <maechler@stat.math.ethz.ch>
1502 :    
1503 :     * R/Auxiliaries.R (dimNamesCheck): added
1504 :    
1505 :     * R/Matrix.R (as.array), (as.vector): new
1506 :    
1507 : maechler 954 2005-09-28 Martin Maechler <maechler@stat.math.ethz.ch>
1508 :    
1509 :     * R/Matrix.R (Matrix): get logical argument 'sparse' with a smart
1510 : maechler 956 default.
1511 :     * R/AllClass.R: move 'factors' slot toplevel "Matrix";
1512 :     "pMatrix" now contains "sparseMatrix"
1513 : maechler 954
1514 : maechler 948 2005-09-26 Martin Maechler <maechler@stat.math.ethz.ch>
1515 :    
1516 :     * tests/Class+Meth.R: new tests; t(t(m)) == m
1517 :    
1518 :     * src/dtCMatrix.c (tsc_transpose): add forgotten "diag" slot
1519 :    
1520 :     * src/dsTMatrix.c (dsTMatrix_as_dsCMatrix): bad typo (segfault!)
1521 :     * src/dtTMatrix.c (dtTMatrix_as_dtCMatrix): new
1522 :    
1523 :     * R/dspMatrix.R: typo in "t" method
1524 :    
1525 : maechler 925 2005-09-18 Douglas Bates <bates@wisc.edu>
1526 :    
1527 :     * R/AllClass.R (TsparseMatrix), CsparseM* and RsparseM*
1528 :     * R/Tsparse.R: instead of R/gTMatrix.R
1529 :     * R/Csparse.R: new
1530 :     * src/Tsparse.c (Tsparse_to_Csparse): new; -> cholmod_()
1531 :     * src/Tsparse.c: new; many trivial methods calling cholmod_()
1532 :     * src/Csparse.c (Csparse_to_Tsparse), transpose, (mat|cross)prod:
1533 :     via cholmod
1534 :    
1535 :     2005-09-16 Martin Maechler <maechler@stat.math.ethz.ch>
1536 :    
1537 :     * R/Auxiliaries.R (non0ind): new function using new C code
1538 :     * src/dgCMatrix.c (compressed_non_0_ij): new utility
1539 :    
1540 : bates 917 2005-09-15 Douglas Bates <bates@localhost.localdomain>
1541 :    
1542 :     * src/chm_common.h: header file required by all C sources that
1543 : maechler 1174 call CHOLMOD functions. It defines a cholmod_common structure
1544 : bates 917 called 'c' whose address is passed as the last argument to
1545 :     (virtually) every CHOLMOD function.
1546 :    
1547 :     * src/Pattern.c: Simple example of the use of CHOLMOD.
1548 :    
1549 :     * src/init.c: initialize and finalize the cholmod_common structure.
1550 :    
1551 :     * src/Makefile: Added source packages CHOLMOD UMFPACK AMD COLAMD
1552 :     LDL and CCOLAMD from the U. of Florida sparse matrix library.
1553 :    
1554 : maechler 908 2005-09-08 Martin Maechler <maechler@stat.math.ethz.ch>
1555 :    
1556 :     * inst/test-tools.R: new file collecting the utility functions used
1557 :     in ./tests/*.R
1558 :    
1559 :     * R/ddenseMatrix.R (cbind2): new methods for "numeric" and "matrix"
1560 :     * R/Matrix.R (cbind2): methods for NULL and missing
1561 :    
1562 : maechler 886 2005-08-31 Martin Maechler <maechler@stat.math.ethz.ch>
1563 :    
1564 :     * R/AllClass.R: new "index" class for "[" and "[<-":
1565 :     First cut at "symmetricMatrix" and "triangularMatrix"
1566 :     * R/gTMatrix.R (.ind.prep): new function;
1567 : maechler 1174 Logical and character indexing now work too.
1568 : maechler 886 * R/Matrix.R: cheap "[<-" methods for denseMatrix now work
1569 :     * tests/indexing.R: new, including *.Rout.save
1570 :     * tests/dgTMatrix.R: new
1571 :    
1572 : bates 876 2005-08-29 Douglas Bates <bates@wisc.edu>
1573 :    
1574 :     * src/dgTMatrix.c (graphNEL_as_dgTMatrix): Corrected the position
1575 :     indicator pos not being updated. Also enforced upper triangular
1576 :     for symmetric case. Need to coerce edges component of elements of
1577 :     edge list - grr! (Why don't they define their classes cleanly?)
1578 :    
1579 : maechler 871 2005-08-26 Martin Maechler <maechler@stat.math.ethz.ch>
1580 :    
1581 :     * R/Matrix.R: added first "[<-" methods; not yet functional
1582 : bates 1352 * R/denseMatrix.R: ditto
1583 : maechler 871 * man/Subassign-methods.Rd: new help file for these
1584 :    
1585 :     2005-08-25 Martin Maechler <maechler@stat.math.ethz.ch>
1586 :    
1587 :     * DESCRIPTION (Version): 0.98-6
1588 :    
1589 :     * R/denseMatrix.R: new file for "[" fallback methods for all dense
1590 :     matrices.
1591 :    
1592 : maechler 868 2005-08-19 Martin Maechler <maechler@stat.math.ethz.ch>
1593 :    
1594 :     * src/lgCMatrix.c (lcsc_to_matrix): new; need for
1595 :     as( <logical>, "matrix")
1596 :    
1597 :     * R/pMatrix.R: coercion to "lgTMatrix"
1598 :    
1599 :     * R/gTMatrix.R: new virtual class to define "[" methods for.
1600 :     * man/gTMatrix-class.Rd:
1601 :     * General slight re-organization of where "[" methods are defined.
1602 :     more to come.
1603 :    
1604 : maechler 871 2005-08-18 Douglas Bates <bates@wisc.edu>
1605 : maechler 868
1606 : maechler 1174 * DESCRIPTION (Version): 0.98-5 released to CRAN
1607 : maechler 871
1608 :     * src/dgTMatrix.c (graphNEL_as_dgTMatrix): add first graphNEL methods
1609 :     * .....
1610 :    
1611 : bates 863 2005-08-18 Douglas Bates <bates@localhost.localdomain>
1612 :    
1613 :     * R/lmer.R: Corrected naming scheme in mcmcsamp to work with lmer
1614 :     or glmer objects.
1615 :    
1616 : maechler 860 2005-08-17 Martin Maechler <maechler@stat.math.ethz.ch>
1617 :    
1618 :     * DESCRIPTION (Version): 0.98-4 : upload to CRAN
1619 :    
1620 :     2005-08-16 Douglas Bates <bates@localhost.localdomain>
1621 :    
1622 :     * R/HBMM.R: finish re-writing R-only code.
1623 :    
1624 : bates 854 2005-08-15 Douglas Bates <bates@localhost.localdomain>
1625 :    
1626 :     * man/externalFormats.Rd: move documentation for writeHB and
1627 :     writeMM here.
1628 :    
1629 :     * src/mmio.c: replace inclusion of <malloc.h> by <stdlib.h>
1630 :     (suggested by Paul Roecker).
1631 :    
1632 :     * tests/validObj.R (assertError): Comment out test that is failing
1633 :     after recent changes in r-devel.
1634 :    
1635 : maechler 860
1636 : maechler 848 2005-08-11 Martin Maechler <maechler@stat.math.ethz.ch>
1637 :    
1638 :     * R/AllClass.R: intermediate virtual class "denseMatrix"
1639 :     * man/denseMatrix-class.Rd
1640 :     * NAMESPACE: export it, and also export
1641 :     * man/unused-classes.Rd: "iMatrix", "zMatrix" and "ldenseMatrix"
1642 :    
1643 : bates 846 2005-08-10 Douglas Bates <bates@wisc.edu>
1644 :    
1645 : maechler 848 * DESCRIPTION (Version): 0.98-3 to CRAN
1646 :    
1647 : bates 846 * src/dtrMatrix.c (dtrMatrix_validate): fixed up validation and
1648 :     matrix_solve code (which was really, really wrong).
1649 :    
1650 : bates 835 2005-08-07 Douglas Bates <bates@wisc.edu>
1651 : maechler 834
1652 :     * DESCRIPTION (Version): 0.98-2
1653 :    
1654 :     * R/HBMM.R (readHB), (readMM): read Matrix Market formats
1655 :    
1656 :     * R/lmer.R (abbrvNms): new
1657 :     * R/lmer.R (mcmcsamp): allow transformed parameters
1658 : bates 835 * src/HBMM.c (Matrix_writeMatrixMarket): Added read/write routines
1659 :     for the Harwell-Boeing and the MatrixMarket formats.
1660 : maechler 834
1661 :     2005-08-04 Martin Maechler <maechler@stat.math.ethz.ch>
1662 :    
1663 :     * man/dtrMatrix-class.Rd: add examples
1664 : bates 835 * man/dtpMatrix-class.Rd: ditto; plus note about PROBLEM
1665 : maechler 834
1666 :     * TODO: note the dtpMatrix (docu) bug
1667 :    
1668 :     * R/zzz.R (.onLoad): assignInNamespace("as.matrix", *, "base")
1669 :     in order to ensure that new as.matrix() is used by old functions,
1670 :     e.g., svd(), qr(), eigen(), dist(),..;
1671 :     apply(), also matplot() or pairs().
1672 :    
1673 :    
1674 :     2005-08-03 Martin Maechler <maechler@stat.math.ethz.ch>
1675 :    
1676 :     * R/lmer.R: add 'fixme' comments and move the linear vs glm check;
1677 :     add comments about 'control' / lmerControl() arguments
1678 :    
1679 : bates 835 2005-07-27 Douglas Bates <bates@wisc.edu>
1680 : bates 820
1681 : bates 835 * man/sleepstudy.Rd: Added the sleep data set.
1682 : maechler 1174 * DESCRIPTION (Version): 0.98-1 released to CRAN
1683 : bates 820
1684 : bates 835 2005-07-12 Douglas Bates <bates@wisc.edu>
1685 : maechler 834 * man/sleepstudy.Rd: Added the sleep data set.
1686 :    
1687 : bates 809 * R/lmer.R (glmmMCMC): Added PACKAGE = "Matrix" in a couple of
1688 :     .Call calls that were producing spurious output.
1689 :    
1690 : bates 835 2005-07-05 Douglas Bates <bates@wisc.edu>
1691 : bates 801
1692 :     * R/lmer.R (lmer): stored updated variance component estimates in
1693 :     mer object for the generalized model. (Bug reported by Renaud
1694 :     Lancelot).
1695 :    
1696 : bates 835 2005-07-03 Douglas Bates <bates@wisc.edu>
1697 : bates 794
1698 :     * src/lmer.c (glmer_devAGQ): Added AGQ for single grouping factor,
1699 :     unidimensional case.
1700 :    
1701 : bates 835 2005-06-08 Douglas Bates <bates@wisc.edu>
1702 : maechler 791
1703 :     * DESCRIPTION (Version): 0.96-1
1704 :    
1705 : maechler 1174 * moved lmer-class' R and C code moved from lme4 to here
1706 : maechler 791
1707 : bates 835 2005-06-04 Douglas Bates <bates@wisc.edu>
1708 : bates 763
1709 :     * R/dgCMatrix.R: Call to csc_matrix_mm used undefined arguments
1710 :     (reported by Guissepe Ragusa <gragusa@ucsd.edu>)
1711 :    
1712 : bates 835 2005-06-02 Douglas Bates <bates@wisc.edu>
1713 : bates 763
1714 :     * src/Makefile.win: Forgot to update this when Makefile changed.
1715 :    
1716 : bates 835 2005-05-11 Douglas Bates <bates@wisc.edu>
1717 : bates 726
1718 :     * src/dgCMatrix.c (csc_transpose): Simplified function fixing a
1719 :     bug reported by Kurt Hornik and Michael Hahsler.
1720 :    
1721 : bates 835 2005-05-10 Douglas Bates <bates@wisc.edu>
1722 : bates 725
1723 :     * src/lgCMatrix.c (Matrix_lgClgCmm): Implementation of methods for
1724 :     logical sparse matrices. These will also be used in the symbolic
1725 :     analysis for lmer objects.
1726 :    
1727 :     * src/dsCMatrix.c (dsCMatrix_matrix_solve): Copied the dimensions
1728 :     of b to the result. Fixes bug reported by Jean.Coursol@math.u-psud.fr
1729 : maechler 791
1730 : bates 835 2005-05-06 Douglas Bates <bates@wisc.edu>
1731 : bates 714
1732 :     * src/dgeMatrix.c (dgeMatrix_colsums): Added an implementation of
1733 :     colMeans, colSums, rowMeans and rowSums.
1734 :    
1735 : bates 835 2005-04-18 Douglas Bates <bates@wisc.edu>
1736 : bates 692
1737 :     * src/lgCMatrix.[ch]: code for _validate method and stub for
1738 :     multiplication operation.
1739 :    
1740 :     * src/dgeMatrix.c (dgeMatrix_matrix_solve): Passing wrong argument
1741 :     to dgetrs.
1742 :    
1743 :     * src/init.c: Fix cut-and-paste error in definition of
1744 :     dgeMatrix_matrix_solve
1745 :    
1746 :     * src/{many files}: Tighten code by using ALLOC_SLOT.
1747 :    
1748 : bates 835 2005-04-15 Douglas Bates <bates@wisc.edu>
1749 : bates 692
1750 :     * R/AllClass.R: Add lgTMatrix and lgCMatrix classes
1751 :    
1752 :     * DESCRIPTION: Eliminate import of stats.
1753 :    
1754 : maechler 791
1755 : bates 835 2005-04-06 Douglas Bates <bates@wisc.edu>
1756 : bates 692
1757 :     * R/AllClass.R : add logical sparse matrix classes
1758 :    
1759 : maechler 687 2005-04-01 Martin Maechler <maechler@stat.math.ethz.ch>
1760 :    
1761 :     * R/dgTMatrix.R: add "[" method for triplet matrices
1762 :     * R/sparseMatrix.R: and other sparse ones; --> add show() for sparse
1763 :    
1764 : bates 835 2005-03-31 Douglas Bates <bates@wisc.edu>
1765 : maechler 687
1766 :     * DESCRIPTION (Version): release 0.95-5 to CRAN
1767 :    
1768 :     * R/dMatrix.R: add %*%, crossprod and solve "fallback" methods
1769 :     * R/sparseMatrix.R: %*%, crossprod()
1770 :     * R/dgeMatrix.R: more "fallback" methods for numeric/dense matrices
1771 :     * man/*.Rd: move method definitions to 'Matrix' and 'dMatrix'
1772 :     * src/lmer.c (lmer_fitted): fix thinko
1773 :    
1774 : maechler 676 2005-03-26 Martin Maechler <maechler@stat.math.ethz.ch>
1775 :    
1776 :     * R/AllClass.R: add two virtual sparse classes ``on top''
1777 :    
1778 :     2005-03-24 Martin Maechler <maechler@stat.math.ethz.ch>
1779 :    
1780 :     * R/AllClass.R (setClass): use "VIRTUAL" for the virtual classes;
1781 :     correspondingly fix examples and tests/ since new()
1782 :     doesn't work for virtual classes.
1783 :    
1784 : maechler 658 2005-03-17 Martin Maechler <maechler@stat.math.ethz.ch>
1785 :    
1786 :     * R/Matrix.R (as.matrix): method and one for unname()
1787 :     * tests/dpoMatrix.R: tests should now be less platform dependent;
1788 :     also run for R 2.1.0; using as.matrix()
1789 :    
1790 : bates 835 2005-03-15 Douglas Bates <bates@wisc.edu>
1791 : maechler 658
1792 :     * R/pMatrix.R: "pMatrix" class added
1793 :     * ....
1794 :    
1795 : bates 835 2005-03-14 Douglas Bates <bates@wisc.edu>
1796 : bates 645
1797 :     * R/dtpMatrix.R: Add unpack method and an example.
1798 :    
1799 :     * src/dsyMatrix.c (dsyMatrix_trf): Add BunchKaufman factorization
1800 :     of general symmetric matrices and associated S4 methods.
1801 :    
1802 : maechler 658 2005-03-10 Martin Maechler <maechler@stat.math.ethz.ch>
1803 :     +
1804 :     2005-03-05 Martin Maechler <maechler@stat.math.ethz.ch>
1805 :    
1806 :     * R/dgeMatrix.R (setAs): and many other files: more coercion,
1807 :     crossprod() and "%*%" methods added; tests, too.
1808 :     * tests/matprod.R: new, for testing these
1809 :    
1810 : bates 835 2005-03-03 Douglas Bates <bates@wisc.edu>
1811 : bates 599
1812 :     * src/lmer.c (lmer_fitted): Added.
1813 :    
1814 : bates 835 2005-03-02 Douglas Bates <bates@wisc.edu>
1815 : bates 596
1816 :     * R/dsTMatrix.R: Conversion from dsTMatrix to dsCMatrix
1817 :    
1818 : bates 835 2005-02-28 Douglas Bates <bates@wisc.edu>
1819 : bates 582
1820 :     * src/*.c,po/,inst/po: Internationalization and localization of
1821 :     the package.
1822 :    
1823 :     * src/ldl.[ch]: Removed these as their contents are referenced in the
1824 :     R_ldl.c file.
1825 :    
1826 :     * src/flame.[ch]: Removed these source files.
1827 : maechler 658
1828 : bates 582 * src/dtrMatrix.c (make_array_triangular): Move to Mutils
1829 :    
1830 :     * src/LU.[ch],src/init.c: absorb in factorizations
1831 :    
1832 :     * src/Mutils.h: prepare for internationalization
1833 :    
1834 :     * src/cblas.h: move the enum definitions to Mutils.h and remove
1835 :     this file
1836 :    
1837 : maechler 578 2005-02-26 Martin Maechler <maechler@stat.math.ethz.ch>
1838 :    
1839 : maechler 579 * R/dgeMatrix.R: provide "dimnames" and "dimnames<-" methods
1840 :    
1841 :     * R/dtrMatrix.R: fix t() method
1842 :    
1843 : maechler 578 * R/dgeMatrix.R: define group methods "Arith", "Math", "Math2"
1844 : maechler 658 * NAMESPACE: export them (and import generics from "methods")
1845 : maechler 578 * tests/group-methods.R : and test them.
1846 :    
1847 :     * src/dtrMatrix.c (dtrMatrix_as_dgeMatrix): prevent seg.fault in
1848 :     border case
1849 :    
1850 :     2005-02-24 Douglas Bates <bates@stat.wisc.edu>
1851 :    
1852 : maechler 658 * DESCRIPTION (Version): 0.95-2 released to CRAN
1853 : maechler 578
1854 :     * src/dgBCMatrix.c:
1855 :     * src/lmer.c: many changes
1856 :     * ...
1857 :    
1858 : maechler 512 2005-02-04 Martin Maechler <maechler@stat.math.ethz.ch>
1859 :    
1860 :     * R/Matrix.R: add more sophisticated show() method.
1861 :    
1862 : maechler 578 2005-02-02 Douglas Bates <bates@stat.wisc.edu>
1863 :    
1864 :     * */* : almost complete reorganization of classes.
1865 :    
1866 : bates 835 2005-01-26 Douglas Bates <bates@wisc.edu>
1867 : bates 460
1868 :     * R/AllGeneric.R: Added matrix exponential generic expm and a method
1869 :     for the geMatrix class.
1870 :    
1871 : bates 835 2005-01-24 Douglas Bates <bates@wisc.edu>
1872 : bates 460
1873 :     * src/Makefile (clean): Remove *.a and *.so
1874 :    
1875 :     * man/cscBlocked-class.Rd: Remove reference to the lmer-class.
1876 :    
1877 : bates 835 2005-01-23 Douglas Bates <bates@wisc.edu>
1878 : bates 460
1879 : maechler 658 * src/lmer.c (Lind): Definition of Lind was backwards. This only
1880 : bates 460 had an effect in cases with more than 2 grouping factors.
1881 :    
1882 : bates 835 2005-01-03 Douglas Bates <bates@wisc.edu>
1883 : bates 415
1884 :     * src/lmeRep.c (lmer_variances): change from lmeRep to lmer
1885 :    
1886 : bates 835 2004-12-23 Douglas Bates <bates@wisc.edu>
1887 : bates 410
1888 :     * src/init.c (R_init_Matrix): Reorder calls to R_registerRoutines
1889 :     and R_useDynamicSymbols (suggested by B.D.Ripley).
1890 :    
1891 : bates 835 2004-12-14 Douglas Bates <bates@wisc.edu>
1892 : bates 392
1893 :     * R/sscMatrix.R: Add determinant methods
1894 :    
1895 :     * src/triplet.[ch],src/init.c (triplet_to_matrix): Add a coercion
1896 :     for tripletMatrix to matrix.
1897 :    
1898 : bates 835 2004-12-13 Douglas Bates <bates@wisc.edu>
1899 : bates 388
1900 : bates 392 * R/AllClass.R (.onLoad): Eliminate the bbCrosstab class, which is
1901 :     no longer used.
1902 :    
1903 : bates 388 * src/R_ldl.c: Created an R-specific version of the ldl.[ch] files
1904 :     with dynamic allocation of scratch arrays.
1905 :    
1906 :     * src/ssclme.c (ssclme_copy_ctab): Fixed bug in creation of ZtZ
1907 :     for multivariate random effects with multiple grouping factors.
1908 :     Fixes part but not all of #15.
1909 :    
1910 : bates 835 2004-12-03 Douglas Bates <bates@wisc.edu>
1911 : bates 375
1912 :     * src/lmeRep.c (lmeRep_factor): order of operations for multiple
1913 :     scalar grouping factors corrected.
1914 :    
1915 : bates 835 2004-11-29 Douglas Bates <bates@wisc.edu>
1916 : bates 375
1917 :     * src/bCrosstab.c: remove diag_update which is no longer used
1918 :    
1919 : bates 835 2004-11-16 Douglas Bates <bates@wisc.edu>
1920 : bates 350
1921 :     * src/Metis_utils.c: Move metis.h include to C sources so that the
1922 :     .h file can be included.
1923 :    
1924 : bates 835 2004-11-12 Douglas Bates <bates@wisc.edu>
1925 : bates 342
1926 : bates 350 * src/LU.c,geMatrix.c,trMatrix.c, etc.:
1927 : bates 342 Complete allocation of slots in NEW_OBJECT.
1928 :    
1929 :     * src/Mutils.h: Moved list of symbols to an include file
1930 :    
1931 : bates 835 2004-11-11 Douglas Bates <bates@wisc.edu>
1932 : bates 342
1933 :     * src/geMutils.c (Matrix_init): remove unused function
1934 :    
1935 : bates 835 2004-11-10 Douglas Bates <bates@wisc.edu>
1936 : bates 342
1937 :     * src/cscMatrix.c (csc_to_imagemat): removed unused function
1938 :    
1939 : bates 835 2004-11-05 Douglas Bates <bates@wisc.edu>
1940 : bates 327
1941 :     * src/Makefile.win (SOURCES_C): Keep consistent with Makefile
1942 :    
1943 : bates 835 2004-10-27 Douglas Bates <bates@wisc.edu>
1944 : bates 303
1945 :     * R/pdmatrix.R: remove PACKAGE="Matrix" in .Call calls
1946 :    
1947 : bates 835 2004-10-04 Douglas Bates <bates@wisc.edu>
1948 : bates 296
1949 :     * src/init.c: Created R_init_Matrix and added registration of C
1950 :     routines.
1951 :    
1952 : bates 835 2004-10-02 Douglas Bates <bates@wisc.edu>
1953 : bates 283
1954 :     * R/tripletMatrix.R: Force a require(lattice) for the image methods.
1955 :    
1956 : bates 835 2004-06-15 Douglas Bates <bates@wisc.edu>
1957 : bates 229
1958 :     * man/trMatrix-class.Rd: Escape the % chars in .Rd files.
1959 :    
1960 : bates 111 2004-04-20 Douglas Bates <bates@stat.wisc.edu>
1961 :    
1962 :     * src/Makefile.win ($(SHLIB)): Modifications per Uwe Ligges.
1963 :    
1964 : bates 109 2004-04-19 Douglas Bates <bates@stat.wisc.edu>
1965 :    
1966 :     * src/ssclme.c (ssclme_update_mm): fix logic error in
1967 :     ssclme_update_mm
1968 :    
1969 : bates 105 2004-04-18 Douglas Bates <bates@stat.wisc.edu>
1970 :    
1971 :     * src/ssclme.c (ssclme_coef, ssclme_coefGets): Create consistency
1972 :     in the order of unconstrained and constrained parameters.
1973 :     (ssclme_gradient): Added the gradients (not yet correct for
1974 :     multidimensional, unconstrained case).
1975 :    
1976 : bates 78 2004-04-14 Douglas Bates <bates@stat.wisc.edu>
1977 :    
1978 :     * src/ssclme.c (ssclme_EMsteps): Fix logic in REML update
1979 :    
1980 :     * src/Makefile.win: Remove unneeded ranlib call
1981 :    
1982 : bates 71 2004-04-12 Douglas Bates <bates@stat.wisc.edu>
1983 :    
1984 :     * DESCRIPTION (Version): New release
1985 :    
1986 :     * src/Makefile.win: Update Makefile.win to umfpack removal.
1987 :    
1988 : bates 49 2004-04-05 Douglas Bates <bates@bates2_home>
1989 :    
1990 :     * src/triplet_to_col.c: Create triplet_to_col as a native
1991 : maechler 658 function, not the version from umfpack. There were problems with
1992 : bates 49 the configuration of UMFPACK for 64-bit processors and there was
1993 :     only one umfpack routine being used so I moved it here.
1994 :    
1995 : bates 45 2004-04-04 Douglas Bates <bates@bates2_home>
1996 :    
1997 :     * src/ssclme.c (ssclme_variances): New function.
1998 :    
1999 : bates 28 2004-03-28 Douglas Bates <bates@bates2_home>
2000 :    
2001 :     * src/ssclme.c (ssclme_fitted): Added function.
2002 :    
2003 : bates 22 2004-03-27 Douglas Bates <bates@bates2_home>
2004 :    
2005 :     * src/ssclme.c (ssclme_transfer_dimnames): Add new function to
2006 :     store the dimnames in the XtX and bVar slots
2007 :     (ssclme_update_mm): Change the dimensions of the bVar slot
2008 :     components and the returned value from ssclme_ranef.
2009 :    
2010 : bates 10 2004-03-18 Douglas Bates <bates@stat.wisc.edu>
2011 :    
2012 :     * R/{pdMat.R,pdIdent.R,pdLogChol.R,pdMatrixLog.R,pdNatural.R},
2013 :     src/{pdMat.c,pdIdent.c,pdLogChol.c,pdNatural.c},
2014 :     tests/{pdCompSymm.R,pdDiag.R,pdIdent.R,pdLogChol.R,pdNatural.R},
2015 :     man/{pdMat-class.Rd,pdmatrix-class.Rd,corrmatrix-class.Rd,
2016 :     pdDiag-class.Rd,pdIdent-class.Rd,pdNatural-class.Rd,
2017 :     pdLogChol-class.Rd,coefGets.Rd,pdCompSymm-class.Rd,
2018 :     pdfactor-class.Rd,pdFactor.Rd,pdMatrix.Rd,
2019 :     pdBlocked-class.Rd},AllClass.R,AllGeneric.R:
2020 :     Moved the pdMat classes from the lme4 package.
2021 :    
2022 :     2004-03-02 Douglas Bates <bates@stat.wisc.edu>
2023 :    
2024 :     * man/ssclme-class.Rd: Update definition and documentation of the
2025 :     ssclme class to include the DIsqrt slot.
2026 :    
2027 :     * src/ssclme.c (ssclme_deviance): Modify order of computation
2028 :     (much faster using dsyrk, a level 3 BLAS routine).
2029 :    
2030 :     * src/Makefile (SUBLIBS): Change definition (K. Hornik)
2031 :    
2032 :     2004-02-28 Douglas Bates <bates@stat.wisc.edu>
2033 :    
2034 :     * tests/ssclme.R: Modify the test to account for the permutation
2035 :     of the levels of the grouping factors.
2036 :    
2037 :     2004-02-23 Douglas Bates <bates@stat.wisc.edu>
2038 :    
2039 :     * R/ssclme.R,src/ssclme.c (ssclme): Move slots of sscCrosstab slot
2040 :     directly into the ssclme class definition.
2041 :    
2042 :     2004-02-22 Douglas Bates <bates@stat.wisc.edu>
2043 :    
2044 :     * DESCRIPTION (Date): New release
2045 :    
2046 :     * man/ssclme-class.Rd: new file.
2047 :    
2048 :     * src/ssclme.c (ssclme_loglik): major revisions in design. It
2049 :     works and it's fast!
2050 :    
2051 :     2004-02-17 Douglas Bates <bates@stat.wisc.edu>
2052 :    
2053 :     * src/taucs/Makefile.win (lib): Change "ar" to "$(AR)" (B.Ripley)
2054 :    
2055 :     2004-02-16 Douglas Bates <bates@stat.wisc.edu>
2056 :    
2057 :     * DESCRIPTION (Date): New release
2058 :    
2059 :     * NAMESPACE: Don't export ssclme.
2060 :    
2061 :     * data/ScotsSec.rda, man/ScotsSec.Rd: Add Scottish secondary
2062 :     school data.
2063 :    
2064 :     2004-02-11 Douglas Bates <bates@stat.wisc.edu>
2065 :    
2066 :     * src/sscCrosstab.c (sscCrosstab): Added a row to the incidence to
2067 :     keep track of the fixed-effects and the response. Counts also
2068 :     gets an extra element, which is always one.
2069 :    
2070 :     * src/ldl.c: Include these routines from Tim Davis' LDL package.
2071 :    
2072 :     2004-02-10 Douglas Bates <bates@stat.wisc.edu>
2073 :    
2074 :     * src/cscMatrix.c (csc_transpose): new function
2075 :    
2076 :     * src/Mutils.c (csc_sort_columns): perm/iperm confusion corrected
2077 :     (csc_components_transpose): new function
2078 :    
2079 :     2004-02-06 Douglas Bates <bates@stat.wisc.edu>
2080 :    
2081 :     * src/triplet.c (triplet_validate): Fix Dim slot on generated
2082 :     triplets
2083 :    
2084 :     2004-01-30 Douglas Bates <bates@stat.wisc.edu>
2085 :    
2086 :     * R/sscCrosstab.R (sscCrosstab): Added sscCrosstab generator function.
2087 :    
2088 :     * src/LU.h (MATRIX_LU_H): Add #ifndef #define ... #endif to this
2089 :     and all other .h files in src.
2090 :    
2091 :     * src/Makefile.win: This and other Makefile.win files contributed
2092 :     by Brian Ripley.
2093 :    
2094 :     2004-01-27 Douglas Bates <bates@stat.wisc.edu>
2095 :    
2096 :     * R/syMatrix.R: Added methods for "%*%".
2097 :    
2098 :     * R/Hilbert.R (Hilbert): Changed Hilbert function to return a
2099 :     poMatrix object.
2100 :    
2101 :     2004-01-26 Douglas Bates <bates@stat.wisc.edu>
2102 :    
2103 :     * man/sscChol-class.Rd,man/mm.Rd,man/y.Rd: Added man pages.
2104 :    
2105 :     2004-01-25 Douglas Bates <bates@bates2_home>
2106 :    
2107 :     * inst/doc/Introduction.Rnw,Comparisons.Rnw: Added vignettes.
2108 :    
2109 :     * R/csc.R: Convert all cscMatrix classes to use Dim slot instead
2110 :     of nrow.
2111 :    
2112 :     2003-12-31 Douglas Bates <bates@stat.wisc.edu>
2113 :    
2114 :     * src/taucs/taucs.h: Moved taucs.h, amd.h, and umfpack.h into
2115 :     subdirectories.
2116 :    
2117 :     2003-12-08 Douglas Bates <bates@stat.wisc.edu>
2118 :    
2119 :     * src/taucs.h: Accidently referred to global header files
2120 :     instead of local files.
2121 :    
2122 :     2003-12-04 Douglas Bates <bates@stat.wisc.edu>
2123 :    
2124 :     * R/AllClass.R: Lots of changes. Removed all the lapack++ code
2125 :     and methods and replaced all classes with S4 classes.
2126 :    
2127 :     2003-04-19 Douglas Bates <bates@stat.wisc.edu>
2128 :    
2129 :     * R/det.R,man/det.Rd: Change name of det generic to determinant
2130 :    
2131 :     * src/R_LapackPP.cc: Change method of calculating determinants
2132 :    
2133 :     2003-02-03 Douglas Bates <bates@stat.wisc.edu>
2134 :    
2135 :     * DESCRIPTION (Version): removed empty data directory as requested
2136 :     by CRAN maintainers. Changed version number and date.
2137 :    
2138 :     2002-10-23 Douglas Bates <bates@stat.wisc.edu>
2139 :    
2140 :     * src/laindex.h: Applied patches from Brian Ripley for compilation
2141 :     under Windows.
2142 :    
2143 :     * Added configure.win and src/Makevars.win as requested by Brian
2144 :     Ripley.
2145 :    
2146 :     2002-05-03 Douglas Bates <bates@stat.wisc.edu>
2147 :    
2148 :     * src/lamatrix.h: Removing pre-1.2.0 compatibility code per Kurt
2149 :     Hornik.
2150 :    
2151 :     2002-04-24 Douglas Bates <bates@stat.wisc.edu>
2152 :    
2153 :     * configure.ac: Replaced configure.in with configure.ac
2154 :     contributed by Kurt Hornik.
2155 :    
2156 :     * aclocal.m4 (ac_clean_files): Replaced this with Kurt Hornik's
2157 :     version for R-1.5.0
2158 :    
2159 : maechler 512
2160 : bates 10 2001-12-10 Douglas Bates <bates@stat.wisc.edu>
2161 :    
2162 :     * man/eigen.Rd: Removed the .Alias in the example

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