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Annotation of /pkg/ChangeLog

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1 : maechler 1947 2007-07-05 Martin Maechler <maechler@stat.math.ethz.ch>
2 :    
3 :     * R/sparseMatrix.R (printSpMatrix): renamed from prSpMatrix()
4 :     and extended with more sophisticated 'col.names' option.
5 :     * NAMESPACE: export printSparseMatrix()
6 :     * man/printSpMatrix.Rd: document, incl. examples
7 :    
8 : maechler 1945 2007-07-04 Martin Maechler <maechler@stat.math.ethz.ch>
9 :    
10 :     * DESCRIPTION (Version): 0.99875-4
11 :    
12 :     * tests/Class+Meth.R (tstMatrixClass): add dimnames, and hence test
13 :     some dimnames perservation.
14 :    
15 :     * R/dsTMatrix.R (t-method): keep dimnames
16 :     * R/dtTMatrix.R: ditto
17 :    
18 :     * R/sparseMatrix.R (prSpMatrix): print colnames when non-trivial
19 :     and ncol(.) < 10
20 :    
21 :     * src/cs_utils.c: drop check_class() and use Matrix_check_class()
22 :     from Mutils.h
23 :    
24 :     * src/lgCMatrix.c ([ln]csc_to_matrix): no longer lose dimnames,
25 :     e.g. in as(<ngCMatrix>, "matrix")
26 :    
27 : maechler 1932 2007-06-29 Martin Maechler <maechler@stat.math.ethz.ch>
28 :    
29 :     * DESCRIPTION (Version): 0.99875-3 ready to be released.
30 :    
31 :     * R/sparseMatrix.R (spMatrix): make spMatrix(3,4) working
32 :    
33 :     * R/AllGeneric.R: set "Math" (and "Math2") group generics in a way
34 :     that should also work in a future version of R.
35 :    
36 : maechler 1922 2007-06-21 Martin Maechler <maechler@stat.math.ethz.ch>
37 :    
38 :     * NAMESPACE, R/AllClass.R: "xsparseVector" class union.
39 :    
40 :     * R/sparseVector.R: more *sparseVector coercions, notably for
41 :     non - double ones.
42 :    
43 : maechler 1911 2007-06-19 Martin Maechler <maechler@stat.math.ethz.ch>
44 :    
45 :     * R/colSums.R: new file for all (col|row)(Sums|Means) methods,
46 :     notably the new ones building on the new .Call(.)s:
47 :    
48 :     * src/dgCMatrix.c (DEF_gCMatrix_COLSUMS): use to define
49 :     all 4 of [dlin]gCMatrix_colSums().
50 :    
51 : bates 1909 2007-06-18 16:12 Douglas Bates <bates@stat.wisc.edu>
52 :    
53 :     * [r4472] src/Syms.h, src/init.c: Added Matrix_lengthSym
54 :     * [r4473] src/dgCMatrix.c: Modified dgCMatrix_colSums for sparseVector
55 :     result
56 : maechler 1911
57 : maechler 1903 2007-06-16 Martin Maechler <maechler@stat.math.ethz.ch>
58 :    
59 : maechler 1904 * R/kronecker.R: fix typo (could lead to inf.recursion)
60 :     * test/simple.R: testing that
61 :    
62 : maechler 1903 * R/sparseMatrix.R (prSpMatrix): change to be used as print()
63 : maechler 1922 method as well (which can have arguments, show() can't).
64 : maechler 1903
65 : bates 1902 2007-06-16 15:52 Douglas Bates <bates@stat.wisc.edu>
66 :    
67 :     * [r4466] R/dgCMatrix.R, src/dgCMatrix.c, src/dgCMatrix.h, src/init.c:
68 :     added dgCMatrix_colSums for [col,row][Sums,Means]
69 :    
70 : bates 1899 2007-06-15 23:15 Douglas Bates <bates@stat.wisc.edu>
71 : bates 1897
72 :     * [r4460] R/sparseMatrix.R, man/dgCMatrix-class.Rd, src/dgCMatrix.c,
73 :     src/dgCMatrix.h, src/init.c: added lm.fit.sparse (unexported),
74 :     coercion of "factor" to "dgCMatrix" and dgCMatrix_cholsol
75 :     * [r4461] R/AllClass.R, man/sparseMatrix-class.Rd: draft "indicators"
76 :     class
77 : bates 1899 * [r4463] R/sparseMatrix.R, man/dgCMatrix-class.Rd,
78 :     man/sparseMatrix-class.Rd: Don't need an "indicators" class - use the
79 :     row names to store the levels - duh! Added an example.
80 : maechler 1903
81 : maechler 1893 2007-06-14 Martin Maechler <maechler@stat.math.ethz.ch>
82 :    
83 :     * src/Csparse.c (Csparse_validate): check for *repeated* entries
84 :     thanks to example from Christian Buchta; with a test here:
85 :     * tests/simple.R:
86 :    
87 : maechler 1886 2007-06-07 Martin Maechler <maechler@stat.math.ethz.ch>
88 :    
89 :     * R/Auxiliaries.R (callGeneric): another fix, needed for some cases
90 :     of colSums(*, sparseResult = TRUE)
91 :    
92 : maechler 1883 2007-06-06 Martin Maechler <maechler@stat.math.ethz.ch>
93 :    
94 :     * R/lsparseMatrix.R, R/ldenseMatrix.R (all, any): change default to
95 :     'na.rm = FALSE' as "everywhere" else in R.
96 :    
97 : bates 1877 2007-06-05 Douglas Bates <bates@stat.wisc.edu>
98 :    
99 : bates 1878 * [r4421] src/CSparse_install.sh: Modify for new organization of
100 : maechler 1883 CSparse package
101 : bates 1877 * [r4425] src/UFsparse_download.sh: Update to version 3.0.0 of
102 :     SuiteSparse
103 :     * [r4426] src/Makefile: add ./UFconfig to the include path for
104 :     compilation
105 : maechler 1883 * [r4427] src/cs.[ch]: update to CSparse version 2.2.0
106 :     * [r4428] inst/doc/UFsparse/* src/{AMD,CHOLMOD,COLAMD}/*
107 :     src/UFconfig/UFconfig.h: Update to version 3.0.0 of SuiteSparse
108 :    
109 : maechler 1870 2007-06-05 Martin Maechler <maechler@stat.math.ethz.ch>
110 :    
111 :     * R/Auxiliaries.R (emptyColnames): + argument msg.if.not.empty, used in
112 :     * R/sparseMatrix.R (prSpMatrix): now gives a message about
113 :     suppressed column names.
114 :    
115 : bates 1868 2007-06-04 17:13 Douglas Bates <bates@stat.wisc.edu>
116 :    
117 :     * [r4418] src/Csparse.c, src/HBMM.c, src/Mutils.c, src/Mutils.h,
118 :     src/Tsparse.c, src/chm_common.c, src/chm_common.h, src/dgCMatrix.c,
119 :     src/dgeMatrix.c, src/dpoMatrix.c, src/dpoMatrix.h, src/dppMatrix.c,
120 :     src/dppMatrix.h, src/dsCMatrix.c, src/dspMatrix.c, src/dspMatrix.h,
121 :     src/dsyMatrix.c, src/dsyMatrix.h, src/dtpMatrix.c, src/dtrMatrix.c:
122 :     Remove warnings after change to const char* CHAR
123 :    
124 :     2007-06-04 17:11 Douglas Bates <bates@stat.wisc.edu>
125 :    
126 :     * [r4417] inst/include/Matrix_stubs.c, inst/include/cholmod.h: Corrected
127 :     type of M_cholmod_ssmult
128 :    
129 : bates 1863 2007-06-03 14:42 Douglas Bates <bates@stat.wisc.edu>
130 :    
131 :     * [r4412] inst/include/Matrix_stubs.c, inst/include/cholmod.h,
132 :     src/init.c: Yet another cholmod export - cholmod_ssmult
133 :    
134 : maechler 1855 2007-05-23 Martin Maechler <maechler@stat.math.ethz.ch>
135 :    
136 :     * NAMESPACE: exported drop0(), since
137 :     * man/drop0.Rd: I have seen several cases, I really wanted to use
138 :     it, so our users may want too.
139 :    
140 :     2007-05-22 Martin Maechler <maechler@stat.math.ethz.ch>
141 :    
142 :     * man/colSums.Rd: separately document colSums() etc, since these
143 :     have the extra argument 'sparseResult'.
144 :    
145 : maechler 1852 2007-05-21 Martin Maechler <maechler@stat.math.ethz.ch>
146 :    
147 :     * R/sparseMatrix.R (spMatrix): utility (T)sparse Matrix constructor;
148 :     * man/spMatrix.Rd: docu., including examples
149 :    
150 :     * R/Auxiliaries.R (sp.colMeans): etc, using a patched callGeneric(),
151 :     in order to make colMeans() etc fast *and* correct.
152 :     * R/sparseVector.R (replSPvec): "[<-" functionality for
153 :     sparseVectors; tested in
154 :     * tests/simple.R:
155 :    
156 :     2007-05-19 Martin Maechler <maechler@stat.math.ethz.ch>
157 :    
158 :     * R/sparseMatrix.R (print.sparseSummary): and summary() method for
159 :     (very) sparse Matrices; output similar to Matlab's print().
160 :    
161 : bates 1847 2007-05-17 Douglas Bates <bates@stat.wisc.edu>
162 :    
163 :     * src/HBMM.c (Matrix_writeMatrixMarket): Write 1-based, not
164 :     0-based, indices (Jose Quesada <quesada@gmail.com>).
165 :    
166 : bates 1844 2007-05-16 Douglas Bates <bates@stat.wisc.edu>
167 :    
168 :     * R/CHMfactor.R: Added solve methods for a CHMfactor object.
169 :    
170 : maechler 1845 2007-05-16 Martin Maechler <maechler@stat.math.ethz.ch>
171 :    
172 :     * R/Auxiliaries.R (sparsapply): new utility, much faster than
173 :     tapply1() for large sparse matrices.
174 :    
175 :     2007-05-15 Martin Maechler <maechler@stat.math.ethz.ch>
176 :    
177 :     * R/Matrix.R (dim<-): reshape now via sparseVector.
178 :    
179 :     * R/sparseVector.R: methods and function for
180 :     * R/AllClass.R: new "sparseVector" class and daughters.
181 :     * NAMESPACE: export new classes
182 :    
183 : maechler 1837 2007-05-14 Martin Maechler <maechler@stat.math.ethz.ch>
184 :    
185 :     * DESCRIPTION (Version): 0.99875-1
186 :     * src/Makefile.win: also remove Lapack code from here (cf. 04-25).
187 :    
188 : maechler 1834 2007-05-11 Martin Maechler <maechler@stat.math.ethz.ch>
189 :    
190 :     * R/Tsparse.R ([, Tsparse): fix last case: *duplicated*, symmetric
191 :     indexing
192 :     * tests/indexing.R: test set for that.
193 :    
194 : maechler 1833 2007-05-08 Martin Maechler <maechler@stat.math.ethz.ch>
195 :    
196 :     * R/Tsparse.R (replTmat): fix the case of *duplicated* index
197 :     entries.
198 :     * tests/indexing.R(out): add regression test for it
199 :    
200 :     2007-04-30 Martin Maechler <maechler@stat.math.ethz.ch>
201 :    
202 :     * R/(l(dense|sparse))?Matrix.R (!): use 'x', not 'e1' as argument
203 :     name for "!" method definitions.
204 :    
205 : maechler 1829 2007-04-26 Martin Maechler <maechler@stat.math.ethz.ch>
206 :    
207 :     * R/Tsparse.R (intI): new utility, used for "[" :
208 :     Cleanup up there, and fixes for duplicated indices - more TODO!
209 :    
210 :     * tests/indexing.R(out): more tests
211 :    
212 : bates 1827 2007-04-25 Douglas Bates <bates@stat.wisc.edu>
213 :    
214 :     * DESCRIPTION,src/Makefile: require R>= 2.5.0 and remove Lapack
215 :     code that is now part of the R Lapack library.
216 : maechler 1829
217 : bates 1827 * src/init.c,inst/include/{Matrix_stubs.c,cholmod.h}:export
218 :     cholmod_factorize_p (used in lme4 for GLMMs and NLMMs).
219 :    
220 : maechler 1829 2007-04-21 Martin Maechler <maechler@stat.math.ethz.ch>
221 :    
222 :     * R/Matrix.R (image): method for all Matrices, not just sparse ones.
223 :    
224 :     2007-04-17 Martin Maechler <maechler@stat.math.ethz.ch>
225 :    
226 :     * R/Auxiliaries.R (tapply1): unname(.) -> colSums() etc don't end
227 :     up with extraneous names '0'...'<n-1>'
228 :    
229 : maechler 1825 2007-04-12 Martin Maechler <maechler@stat.math.ethz.ch>
230 :    
231 :     * R/dgTMatrix.R (mat2dgT): care about NAs
232 :    
233 :     2007-04-11 Martin Maechler <maechler@stat.math.ethz.ch>
234 :    
235 :     * R/kronecker.R: triangularity preserving methods
236 :    
237 : maechler 1803 2007-03-27 Martin Maechler <maechler@stat.math.ethz.ch>
238 :    
239 :     * R/kronecker.R: new file collecting kronecker() methods in one
240 :     place. Goal: become much faster!
241 :    
242 : maechler 1799 2007-03-23 Martin Maechler <maechler@stat.math.ethz.ch>
243 :    
244 :     * src/dtCMatrix.c (dtCMatrix_solve): use the new code from Kasper
245 :     Kristensen based cs_spsolve() instead of _lsolve & _usolve which
246 :     can be much faster.
247 :    
248 :     * tests/matprod.R: add regression tests for these (upper & lower).
249 :    
250 :     2007-03-19 Martin Maechler <maechler@stat.math.ethz.ch>
251 :    
252 :     * R/Matrix.R (diff): method for our Matrices.
253 :    
254 :     * R/sparseMatrix.R (isDiagonal): check dim()!
255 :    
256 :     2007-03-17 Martin Maechler <maechler@stat.math.ethz.ch>
257 :    
258 :     * R/Matrix.R (dim<-): new method for "reshape()" built on a
259 :     proposal from Tamas Papp.
260 :    
261 :     2007-03-16 Martin Maechler <maechler@stat.math.ethz.ch>
262 :    
263 :     * R/AllGeneric.R: remove all if(!isGeneric(.)) clauses
264 :    
265 :     * R/zzz.R (.onLoad, .onUnload): do *not* leave bind_activation(TRUE);
266 : maechler 1803 rather define and export cBind() and rBind() only.
267 :     --> useRs *must* change code that used to have cbind()/rbind() !!
268 : maechler 1799
269 : maechler 1803 * R/bind.R: change tests from cbind() to cBind() and similarly to rBind()
270 :     * R/bind.Rout.save: ditto
271 : maechler 1799
272 : bates 1787 2007-02-16 Douglas Bates <bates@r-project.org>
273 :    
274 :     * DESCRIPTION (Date, Version): 0.9975-11 with new date
275 :     * src/dgCMatrix.c (R_to_CMatrix, compressed_to_TMatrix): remove
276 :     const modifier on declaration of the array 'valid'
277 :    
278 : bates 1786 2007-02-12 Douglas Bates <bates@stat.wisc.edu>
279 :    
280 :     * R/CHMfactor.R: Add image method (coercion to sparseMatrix).
281 :    
282 : maechler 1765 2007-02-05 Martin Maechler <maechler@stat.math.ethz.ch>
283 :    
284 : maechler 1768 * DESCRIPTION (Date, Version): 0.9975-10 with new date.
285 :    
286 : maechler 1767 * R/Ops.R (Arith): make sure Csparse o Csparse also works for e.g. ntCMatrix
287 :     * tests/simple.R: test the above and some of these coercions:
288 :    
289 :     * R/nsparseMatrix.R: coercing "Csparse" to "lsparseMatrix";
290 :     be careful to avoid infinite recursion, using new coercions in
291 :     * R/ngCMatrix.R and nsC... and ntC...
292 :     * R/lsparseMatrix.R: ditto
293 :    
294 : maechler 1765 * R/SparseM-conv.R: more conversion, notably for triplet matrices.
295 :    
296 : maechler 1767 * src/dgCMatrix.c (R_to_C_Matrix): port Doug's fix and
297 :     * R/Rsparse.R: reactivate .Call()s
298 : maechler 1765
299 : maechler 1767 * tests/Class+Meth.R: a bit more on actual classes
300 :    
301 :     2007-02-04 Douglas Bates <bates@stat.wisc.edu>
302 :    
303 :     * src/dgCMatrix.c (compressed_to_TMatrix): fix memory bug using strdup()
304 :    
305 : maechler 1760 2007-02-03 Martin Maechler <maechler@stat.math.ethz.ch>
306 : maechler 1758
307 :     * DESCRIPTION (Version): 0.9975-10 to upload
308 :    
309 : maechler 1760 * tests/Class+Meth.R (tstMatrixClass): require coercions to
310 :     specific classes less unconditionally.
311 :    
312 :     * R/Auxiliaries.R: get rid of as_Tsparse() and as_Rsparse()
313 :    
314 :     * R/Tsparse.R (triu): etc, use as(*, "TsparseMatrix") instead of as_Tsparse()
315 :    
316 :     * R/Rsparse.R (.R.2.T): R-level workaround using compressed_to_TMatrix.
317 : maechler 1758 * R/Rsparse.R (.R.2.C): R-level workaround since C-level
318 :     R_to_CMatrix segfaults on one platform.
319 : maechler 1760 Eliminate most coercion method to *specific* classes, and replace
320 :     with virtual classes coercions.
321 : maechler 1758
322 : maechler 1760
323 : maechler 1758 2007-02-01 Martin Maechler <maechler@stat.math.ethz.ch>
324 :    
325 :     * src/init.c: export the CHM...._validate() placeholders, since
326 :     they *are* called.
327 :    
328 : maechler 1760 * tests/Class+Meth.R (classCanCoerce): and starting to test
329 : maechler 1758 all as(<from>, <to>)
330 :    
331 : maechler 1751 2007-01-30 Martin Maechler <maechler@stat.math.ethz.ch>
332 :    
333 :     * R/Tsparse.R ([): more care when subsetting triangular Tsparse
334 :     * tests/indexing.R: tested now
335 :     * tests/indexing.Rout.save: updated
336 :    
337 :     * src/Csparse.c (Csparse_to_dense): use Rkind = -1 for PATTERN to
338 :     * src/chm_common.c (chm_dense_to_SEXP): return "ngeMatrix" when
339 :     appropriate.
340 :    
341 :     * NAMESPACE: export a trivial
342 :     * R/Matrix.R: drop() Matrix-method
343 :    
344 :     * R/AllClass.R: moved all prototypes to virtual super classes.
345 :    
346 :     * R/Rsparse.R: many more coercions to have less exceptions in
347 :     * tests/Class+Meth.R:
348 :    
349 :     * R/Ops.R (Compare): tweak for case with NA
350 :     * tests/simpl.R: hence another 'FIXME' eliminated
351 :    
352 : maechler 1747 2007-01-29 Martin Maechler <maechler@stat.math.ethz.ch>
353 :    
354 : maechler 1748 * R/diagMatrix.R (solve): the obvious methods for diagonalMatrix
355 :     objects.
356 :    
357 : maechler 1747 * tests/Class+Meth.R (tstMatrixClass): now testing diag(), nnzero(),
358 :     and more of "!", "&", "|", all, any; coercions
359 :    
360 :     * R/Rsparse.R: many coercions (which enable quite a few other
361 :     methods), thanks to enhancements in
362 :     * src/dgCMatrix.c (R_to_CMatrix): new, and
363 :     * src/dgCMatrix.c (compressed_to_TMatrix): now for (d,l,n) ,
364 :     symmetric & triangular and ..RMatrix objects.
365 :    
366 :     * src/TMatrix_as.c (Matrix_T_as_DENSE,Matrix_T_as_GENERAL):
367 :     renamed file from src/dsTMatrix.c;
368 :     now dealing with symmetric and triangular Tsparse coercions, both
369 :     to dense and general.
370 :    
371 :     2007-01-27 Martin Maechler <maechler@stat.math.ethz.ch>
372 :    
373 :     * src/dsTMatrix.c: has now "l" and "n" methods besides the "d" ones.
374 :    
375 :     * R/Ops.R (Arith): <dgCMatrix> o <numeric> now remains sparse
376 :     where sensible when the <numeric> is of length > 1.
377 :    
378 :     2007-01-26 Martin Maechler <maechler@stat.math.ethz.ch>
379 :    
380 :     * R/Matrix.R ([<-): for M[] <- value: fix length
381 :    
382 :     2007-01-25 Martin Maechler <maechler@stat.math.ethz.ch>
383 :    
384 :     * R/Auxiliaries.R (n2l_Matrix): new, to be used in
385 :     * R/ndenseMatrix.R: new coercions n* -> l*
386 :    
387 : maechler 1738 2007-01-22 Martin Maechler <maechler@stat.math.ethz.ch>
388 :    
389 :     * R/triangularMatrix.R: new file; simple triu() and tril() methods.
390 :    
391 :     * R/Ops.R ("Logic"): and other "Ops", many updates
392 :    
393 :     2007-01-18 Martin Maechler <maechler@stat.math.ethz.ch>
394 :    
395 :     * src/Mutils.h (SET_DimNames): new utility
396 :    
397 :     * R/Auxiliaries.R (nnzero): improved and now exported via
398 :    
399 :     * NAMESPACE: + nnzero(); length() == prod(dim(.)) method for all "Matrix" objects
400 :    
401 : maechler 1725 2007-01-17 Martin Maechler <maechler@stat.math.ethz.ch>
402 :    
403 :     * R/diagMatrix.R (!): fix typo.
404 :    
405 :     2007-01-16 Martin Maechler <maechler@stat.math.ethz.ch>
406 :    
407 :     * R/Auxiliaries.R (as_Csparse): and quite a few others:
408 :     allow to pass class definition --> speedup
409 :     * R/sparseMatrix.R: apply the above
410 :    
411 :     * R/Csparse.R: coercion Csparse* to dense* now preserves shape properties.
412 :    
413 :     * src/Mutils.h (mMatrix_as_geMatrix): new, based on
414 :     * src/Mutils.c (dup_mMatrix_as_geMatrix): new; generalization of
415 :     old dup_mMatrix_as_dgeMatrix), eliminating a long-standing "FIXME".
416 :    
417 :     * src/dense.c (dense_to_Csparse): use new mMatrix_as_geMatrix()
418 :    
419 :     * R/denseMatrix.R (.dense2C): based on dense_to_Csparse: name it,
420 :     and use it for "sparse*" as well, since it's faster than the
421 :     as_Csparse(.) way.
422 :    
423 :     2007-01-15 Martin Maechler <maechler@stat.math.ethz.ch>
424 :    
425 :     * R/Ops.R ("Logic"): more methods, notably an <lgC> o <lgC> one.
426 :    
427 : maechler 1724 2007-01-12 Martin Maechler <maechler@stat.math.ethz.ch>
428 :    
429 :     * R/Tsparse.R (.TM.repl.i.2col): new internal function to be used
430 :     as method for M[ ij ] <- v
431 :     * R/Csparse.R:: go via Tsparse for "M[ij] <- v"
432 :    
433 :     * R/Ops.R: "Compare" for (C|R)sparse: need pointer slot for all
434 :     FALSE answer
435 :    
436 :     * R/Csparse.R (replCmat): fix the "all non-zero" case with reordering
437 :     * tests/indexing.R: test it, and some of the above
438 :    
439 :     2007-01-05 Martin Maechler <maechler@stat.math.ethz.ch>
440 :    
441 :     * R/Auxiliaries.R (is_duplicatedT): new utility
442 :    
443 : bates 1716 2007-01-05 Douglas Bates <bates@stat.wisc.edu>
444 :    
445 :     * src/init.c (R_init_Matrix): export cholmod_scale
446 :    
447 : maechler 1724 2006-12-30 Martin Maechler <maechler@stat.math.ethz.ch>
448 :    
449 :     * R/zzz.R (tmp): for R >= 2.5.0, extend formals of our
450 :     base::as.matrix to (x, ...)
451 :    
452 : maechler 1714 2006-12-28 Martin Maechler <maechler@stat.math.ethz.ch>
453 :    
454 :     * R/Ops.R ("Arith" etc): move almost all "Ops" methods to new R
455 :     file; start using "Logic", hence
456 :    
457 :     * DESCRIPTION (Depends): R >= 2.4.1 (since we want "Logic")
458 :     * NAMESPACE: import and export "Logic"
459 :    
460 :     2006-12-27 Martin Maechler <maechler@stat.math.ethz.ch>
461 :    
462 :     * src/zpotfr.f and dependencies: use LAPACK 3.1 version
463 :     only needed previously to R version 2.5.0.
464 : maechler 1724
465 : maechler 1710 2006-12-26 Martin Maechler <maechler@stat.math.ethz.ch>
466 :    
467 :     * DESCRIPTION (Date, Version): 0.9975-8, ready for release
468 :    
469 :     * R/Tsparse.R (replTmat): fix subassignment of triangular
470 :     * R/Csparse.R (replCmat): ditto
471 :     * tests/indexing.R: more tests, incl the above fix
472 :    
473 :     2006-12-23 Martin Maechler <maechler@stat.math.ethz.ch>
474 :    
475 :     * R/Auxiliaries.R (drop0): extend for non CSparse
476 :     * R/Auxiliaries.R (diagU2N): should work for all sparseMatrix
477 :    
478 :     * src/Csparse.c (Csparse_to_Tsparse, Csparse_general_to_symmetric):
479 :     use uplo correctly (!); other places: use uplo_P() macro
480 :    
481 :     * R/Csparse.R (replCmat): call diagU2N() when needed
482 :     * R/Tsparse.R (replTmat): ditto
483 :    
484 :     * src/dtCMatrix.c (tCMatrix_validate): new
485 :     * src/dtTMatrix.c (tTMatrix_validate): new, used in
486 :     * R/AllClass.R: for validity of dtC, dsC, and dtT, dsT.
487 :    
488 :     * R/diagMatrix.R (replDiag): to use in [<-
489 :    
490 : maechler 1708 2006-12-22 Martin Maechler <maechler@stat.math.ethz.ch>
491 :    
492 :     * R/Auxiliaries.R (as_Csparse2, as_geSimpl): new functions;
493 :     also more general diagU2N().
494 :    
495 :     2006-12-21 Martin Maechler <maechler@stat.math.ethz.ch>
496 :    
497 :     * R/bind2.R: new file for all cbind2(), rbind() methods moved here
498 :     from R/<foo>Matrix.R files. Better diagonal & improved sparse methods.
499 :    
500 : maechler 1707 2006-12-20 Martin Maechler <maechler@stat.math.ethz.ch>
501 :    
502 :     * tests/bind.R: a few more cases
503 :     * R/Auxiliaries.R (.M.kind): also work for atomic vectors
504 :    
505 :     * R/denseMatrix.R (cbind2/rbind2): moved here (and generalized) from
506 :     * R/ddenseMatrix.R (cbind2/rbind2)
507 :     * R/Tsparse.R (replTmat): final(?!) fix for "[<-" ..
508 :     * tests/indexing.R
509 :     * tests/indexing.Rout.save: updated
510 :    
511 :     2006-12-18 Martin Maechler <maechler@stat.math.ethz.ch>
512 :    
513 :     * R/Tsparse.R (replTmat): fixed a remaining "[<-" bug in
514 :     * tests/indexing.R
515 :    
516 : maechler 1705 2006-12-15 Martin Maechler <maechler@stat.math.ethz.ch>
517 :    
518 :     * R/sparseMatrix.R (prSpMatrix): "." alignment much improved:
519 :     align with proper position of "0", i.e., right for integers.
520 :     argument 'align' by default is "fancy".
521 :    
522 :     2006-12-14 Martin Maechler <maechler@stat.math.ethz.ch>
523 :    
524 :     * R/sparseMatrix.R: delegate "Compare" to "Csparse.."
525 :     * R/Csparse.R: and fix "Compare" for more cases.
526 :     * tests/Class+Meth.R: test some of these (m == m, m != m)
527 :    
528 :     2006-12-13 Martin Maechler <maechler@stat.math.ethz.ch>
529 :    
530 :     * R/lsparseMatrix.R: all() and any() methods
531 :     * R/ldenseMatrix.R: ditto
532 :     * NAMESPACE, R/Matrix.R: ditto
533 :    
534 :     * man/all-methods.Rd: document them minimally
535 :    
536 :     * tests/simple.R: add a few examples for these
537 :    
538 : maechler 1696 2006-12-11 Martin Maechler <maechler@stat.math.ethz.ch>
539 :    
540 :     * R/Tsparse.R ([): fix long standing typo in symmetric case
541 :     * man/dsCMatrix-class.Rd: add example exhibiting the above case
542 :    
543 : bates 1691 2006-12-10 Douglas Bates <bates@stat.wisc.edu>
544 :    
545 :     * src/CHMfactor.c (CHMfactor_to_sparse): change LDL factorization
546 :     to LL before converting to a sparse matrix. (The LDL form can be
547 :     converted to a sparse matrix but it is implicitly a unit
548 :     triangular matrix and a diagonal matrix overwritten on the diagonal.)
549 :    
550 :     2006-12-09 Douglas Bates <bates@stat.wisc.edu>
551 :    
552 :     * src/chm_common.c (chm_factor_to_SEXP): allocate and fill the Dim slot.
553 :    
554 : bates 1688 2006-12-08 Douglas Bates <bates@stat.wisc.edu>
555 :    
556 :     * DESCRIPTION (Version): updated -> release 0.9975-7
557 :     * src/{init.c,chm_common.c}, inst/include/*: export cholmod_analyze_p
558 :    
559 : maechler 1682 2006-11-30 Martin Maechler <maechler@stat.math.ethz.ch>
560 :    
561 :     * R/diagMatrix.R (%*%): write a direct [diag o Csparse] method
562 :    
563 : bates 1681 2006-11-29 Douglas Bates <bates@stat.wisc.edu>
564 :    
565 :     * src/dgeMatrix.c (dgeMatrix_solve): Check error code from dgetri.
566 :     * tests/dg_Matrix.R: Add Barry Rowlingson's test of a matrix that
567 :     is exactly singular.
568 :    
569 : maechler 1674 2006-11-07 Martin Maechler <maechler@stat.math.ethz.ch>
570 :    
571 :     * DESCRIPTION (Date): updated -> release 0.9975-6
572 :    
573 : maechler 1673 2006-11-06 Martin Maechler <maechler@stat.math.ethz.ch>
574 :    
575 :     * R/Csparse.R (replCmat): symmetric indexing of symmetric matrix
576 :     now returns symmetric.
577 :    
578 :     * R/zzz.R ("diag<-"): replace "diag<-" in base for R <= 2.4.x
579 :    
580 :     * R/Matrix.R (.M.sub.i.2col): new, for M[ cbind(i,j) ] indexing.
581 :     * R/Matrix.R (.M.repl.i.2col): new, for M[ cbind(i,j) ] <- value
582 :    
583 :     * R/Auxiliaries.R (.type.kind): added
584 :    
585 :     2006-11-04 Martin Maechler <maechler@stat.math.ethz.ch>
586 :    
587 :     * src/cs.[ch]: updated to CSparse Version 2.0.3 by simply
588 :     running src/CSparse_install.sh
589 :    
590 :     * R/denseMatrix.R: "[": keep symmetric on symmetric indexing.
591 :    
592 : maechler 1665 2006-11-03 Martin Maechler <maechler@stat.math.ethz.ch>
593 :    
594 :     * src/dsCMatrix.c (dsCMatrix_Csparse_solve): new
595 :     * R/dsCMatrix.R (solve): "fully-sparse" using the above.
596 :    
597 :     * R/AllClass.R: "pMatrix" now also inherits from "generalMatrix"
598 :    
599 :     * tests/Class+Meth.R (tstMatrixClass): now assure
600 :     the (important in method programming) property :
601 :    
602 :     ###>> Every "Matrix" is either
603 :     ###>> "general*", "symmetric*", "triangular*" or "diagonal*"
604 :    
605 :     (where "*" stands for "Matrix")
606 :    
607 :     * R/Auxiliaries.R (diagU2N): now .Call()s Csparse_diagU2N for <Csparse>
608 :    
609 :     * R/dMatrix.R (Compare(<dMatrix>,<dMatrix>): update and
610 :     * tests/validObj.R: checks for "comparison"
611 :    
612 :     * R/sparseMatrix.R ([): improved indexing for sparse;
613 :     trying to keep <symmetric>[ n, n] symmmetric
614 :    
615 :     * tests/indexing.R: indexing for logical sparse now ok
616 :    
617 :    
618 : maechler 1660 2006-11-02 Martin Maechler <maechler@stat.math.ethz.ch>
619 :    
620 : maechler 1661 * src/Tsparse.c: use xTsparse_validate() , and hence remove
621 :    
622 :     * src/{ltC,lsC,lgT}Matrix.[ch]: removed
623 :    
624 :     2006-11-02 Martin Maechler <maechler@stat.math.ethz.ch>
625 :    
626 : maechler 1660 * R/AllClass.R (Matrix-class): check length of dimnames in validity.
627 :    
628 :     * tests/simple.R: validObject() checking the above.
629 :    
630 : maechler 1665 * src/dgCMatrix.c (xCMatrix_validate): new, small and simple,
631 : maechler 1660 replacing both dgCMatrix_validate and lgCM*.
632 :    
633 :     * src/Csparse.c (Csparse_dense_prod, etc): do not lose dimnames;
634 :     fix dimnames setting in other places.
635 :     * src/chm_common.c (chm_dense_to_SEXP): now can pass dimnames
636 :    
637 : maechler 1659 2006-11-01 Martin Maechler <maechler@stat.math.ethz.ch>
638 :    
639 : maechler 1660 * R/Csparse.R,src/Csparse.c, etc: tcrossprod(<CsparseM>,<CsparseM>)
640 :    
641 :     * R/sparseMatrix.R (isSymmetric): drop 'factors' slot for
642 :     symmetry test, via
643 : maechler 1659 * R/Auxiliaries.R (.as.dgC.0.factors):
644 :    
645 : bates 1657 2006-11-01 Douglas Bates <bates@r-project.org>
646 :    
647 :     * R/Csparse.R,src/Csparse.c,tests/matprod.R,
648 :     man/CsparseMatrix-class.Rd: crossprod(<CsparseMatrix>,
649 :     <CsparseMatrix>) added
650 :    
651 : maechler 1655 2006-10-30 Martin Maechler <maechler@stat.math.ethz.ch>
652 :    
653 :     * tests/matprod.R: add a variation of Harri's example
654 :    
655 :     * R/dsparseMatrix.R: fix crossprod(<dsparse>, <dge>) to *not*
656 :     recursive infinitely.
657 :    
658 :     * R/dgCMatrix.R: + solve(<sparse>, <sparse>)
659 :    
660 :     * tests/indexing.R: add test for the "<" bug fixed 10-27 in R/dMatrix.R
661 :    
662 :     2006-10-28 Martin Maechler <maechler@stat.math.ethz.ch>
663 :    
664 :     * tests/Class+Meth.R (tstMatrixClass): more: use non-trivial
665 :     matrix if possible; test m+m == 2*m; now test dgRMatrix.
666 :     * R/dgRMatrix.R (.to.dgR): a few more coercions, in order to
667 :     satisfy the above test.
668 :    
669 : maechler 1654 2006-10-27 Martin Maechler <maechler@stat.math.ethz.ch>
670 :    
671 : maechler 1655 * R/Matrix.R (Ops): <Matrix> o <matrix> method added
672 :    
673 : maechler 1654 * R/dgCMatrix.R: solve(a, b="missing") based on
674 :     * src/dgCMatrix.c (dgCMatrix_matrix_solve): extend to work with
675 :     RHS = NULL.
676 :    
677 :     * R/diagMatrix.R (diagdiagprod): extend %*% etc to ldiMatrix;
678 :     add more (needed) [t]crossprod() methods.
679 :    
680 :     * man/ddiMatrix-class.Rd: more info, notably on 'diag'
681 :    
682 :     * R/Auxiliaries.R (as_CspClass): cleanup
683 :     (drop0): internal utility for "Csparse_drop(*, 0)"
684 :     (.bail.out.2): encourage active feedback
685 :    
686 :     2006-10-26 Martin Maechler <maechler@stat.math.ethz.ch>
687 :    
688 :     * R/dMatrix.R(Compare): new(), then slots [no validity check]
689 :    
690 :     * src/Csparse.c (Csparse_validate): fixed (and more efficient in
691 :     non-valid or 'sorted' case).
692 :    
693 :     * R/dsparseMatrix.R: add "chol" method.
694 :     * R/ddenseMatrix.R: ditto
695 :    
696 :     * R/diagMatrix.R (Ops): group methods for <diagonal> o <sparse>
697 :     * NAMESPACE (Ops)
698 :     * R/diagMatrix.R (diag2T): simple utility used "higher level"
699 :     coercion; deprecating direct lower level coercions.
700 :    
701 :     * R/*.R (seq): use seq_len() and seq_along() where possible.
702 :    
703 :    
704 : maechler 1647 2006-10-23 Martin Maechler <maechler@stat.math.ethz.ch>
705 :    
706 :     * DESCRIPTION (Version): 0.9975-5 ready for release
707 :    
708 : bates 1646 2006-10-20 Douglas Bates <bates@stat.wisc.edu>
709 :    
710 :     * src/init.c (R_init_Matrix): export more cholmod CCallable functions.
711 :    
712 : maechler 1642 2006-10-20 Martin Maechler <maechler@stat.math.ethz.ch>
713 :    
714 :     * R/AllClass.R (corMatrix): add 'validity' check;
715 :     comment out unused "LDL" class definition
716 :     * NAMESPACE: mention, but do not export "LDL" class
717 :     * R/corMatrix.R: new (simple), needed for R-devel with
718 :     * tests/Class+Meth.R (tstMatrixClass): 1 exception for corMatrix
719 :     coerce and t() exceptions for all 5 'Mat.MatFact' classes.
720 :    
721 : bates 1641 2006-10-19 Douglas Bates <bates@stat.wisc.edu>
722 :    
723 :     * src/chm_common.h: Add R_cholmod_start to initialize cholmod to
724 :     use Rprintf and R's error handling.
725 :    
726 : maechler 1635 2006-10-17 Martin Maechler <maechler@stat.math.ethz.ch>
727 :    
728 :     * R/diagMatrix.R (%*%): rep(*, each = .) in Matrix %*% diagonal.
729 :     * tests/matprod.R: add tests for the bug fixed.
730 :    
731 : bates 1624 2006-10-11 Douglas Bates <bates@stat.wisc.edu>
732 :    
733 :     * src/HBMM.[ch]: remove HarwellBoeing format for writing.
734 :     * src/SOURCES_C.mkf (SOURCES_C): no longer compile iohb.c
735 :    
736 :     2006-10-06 Douglas Bates <bates@stat.wisc.edu>
737 :    
738 : bates 1629 * R/d[gs]CMatrix.R: deprecate the writeHB function. Use writeMM instead.
739 : bates 1624
740 : maechler 1618 2006-10-06 Martin Maechler <maechler@stat.math.ethz.ch>
741 :    
742 :     * DESCRIPTION (Version): 0.9975-3
743 :    
744 :     * R/diagMatrix.R (bdiag): new function constructing block diagonal
745 :     (sparse) matrices.
746 :     * man/bdiag.Rd: docu + examples
747 :    
748 : maechler 1619 * R/Csparse.R (replCmat): calling new Csparse_drop() now.
749 :    
750 : maechler 1618 * src/Csparse.c (Csparse_general_to_symmetric, Csparse_drop): new functions
751 :     * R/lsCMatrix.R: three more coercions to lsC (thanks to the above)
752 :    
753 :     * R/diagMatrix.R (Diagonal): '[<-' method for diag.matrices such
754 :     that result is sparse or diagonal (and not dense).
755 :    
756 :     * man/Subassign-methods.Rd: fix examples
757 :    
758 :     * R/Matrix.R (Matrix): Matrix(0, *) or Matrix(*, sparse=TRUE)
759 :     should always return a sparse (and not sometimes a diagonal) matrix.
760 :    
761 : maechler 1615 2006-10-05 Martin Maechler <maechler@stat.math.ethz.ch>
762 :    
763 :     * R/Matrix.R ([<-): also for value "Matrix" or "matrix"
764 :    
765 : bates 1613 2006-10-04 Douglas Bates <bates@stat.wisc.edu>
766 :    
767 :     * DESCRIPTION (Version): 0.9975-2
768 : maechler 1615
769 : bates 1613 * inst/include/Matrix_stubs.c (M_cholmod_sparse_to_triplet): export more symbols
770 :    
771 : bates 1611 2006-10-02 Douglas Bates <bates@R-project.org>
772 :    
773 :     * tests/dg_Matrix.R: Simplify test taking into account new code.
774 :    
775 : maechler 1599 2006-09-29 Martin Maechler <maechler@stat.math.ethz.ch>
776 :    
777 : maechler 1600 * R/Csparse.R (replCmat): improve for missing i / j in non-simple cases
778 :    
779 : maechler 1599 * R/lsTMatrix.R: new files w/ missing methods
780 :     * R/nsTMatrix.R: " 'for completeness'
781 :    
782 :     * tests/Class+Meth.R: a bit less 'not.ok.classes'
783 :    
784 :     * R/Tsparse.R (t): generalized "t" method from "dgT*" to "Tsparse*"
785 :    
786 :    
787 : bates 1595 2006-09-28 Douglas Bates <bates@R-project.org>
788 :    
789 :     * src/dppMatrix.h: Ensure definition of dspMatrix_validate is
790 :     included.
791 :    
792 :     * src/init.c, inst/include/{Matrix.h,Matrix_stubs.h,cholmod.h}:
793 :     Export C-callable functions used in Zt_create in lme4.
794 :    
795 : maechler 1592 2006-09-28 Martin Maechler <maechler@stat.math.ethz.ch>
796 :    
797 :     * DESCRIPTION (Version): 0.9975-1
798 :    
799 :     * tests/simple.R: less checks fail; using NA, found that our
800 :     kronecker() is not base-compatible with NA's.
801 :    
802 :     * R/dMatrix.R: "Compare" method now implemented for all cases
803 :    
804 :     * R/Auxiliaries.R (indTri): == which([lower/upper].tri( * )) new utility
805 :    
806 :     * man/dtpMatrix-class.Rd: mention length of 'x' slot
807 :    
808 :     * src/dtpMatrix.c (dtpMatrix_validate): fix check
809 :     * src/dspMatrix.c (dspMatrix_validate): ditto
810 :    
811 :     * R/dtTMatrix.R (gt2tT): fix ("l" -> "n")
812 :     including coercion to [nl]tTMatrix.
813 :    
814 :     * R/diagMatrix.R (show): print a header line as for other classes.
815 :    
816 :     2006-09-27 Martin Maechler <maechler@stat.math.ethz.ch>
817 :    
818 :     * src/Makefile.win (SUBDIRS): fix typo
819 :    
820 : maechler 1583 2006-09-19 Martin Maechler <maechler@stat.math.ethz.ch>
821 :    
822 :     * DESCRIPTION (Date): ready to release 0.9975-0 to CRAN
823 :    
824 : bates 1577 2006-09-18 Douglas Bates <bates@stat.wisc.edu>
825 :    
826 :     * R/[CT]sparse.R (crossprod and tcrossprod): Handle the cases for x
827 :     symmetric and y missing in R code using %*% (cholmod_aat doesn't
828 :     accept a symmetric matrix).
829 :     * tests/group-methods.R: Uncomment test of crossprod applied to
830 :     lsCMatrix objects.
831 :    
832 : maechler 1575 2006-09-18 Martin Maechler <maechler@stat.math.ethz.ch>
833 :    
834 :     * R/AllClass.R (symmetricMatrix): add validity method (available
835 :     in C for a long time). Many "n..Matrix": drop (wrong) validity arg.
836 :    
837 :     * src/lgCMatrix.c (lgCMatrix_validate): check 'x' slot (!)
838 :    
839 :     * tests/indexing.Rout.save:
840 :     * tests/indexing.R: additions, mainly for 'lsparse'
841 :    
842 :     * R/diagMatrix.R (Diagonal) & coercion to lgTMatrix: fixes for NA
843 :     case.
844 :    
845 :     * R/Auxiliaries.R (nz.NA): new utility now used in nnzero()
846 :    
847 : maechler 1571 2006-09-16 Martin Maechler <maechler@stat.math.ethz.ch>
848 :    
849 : maechler 1572 * R/sparseMatrix.R (prSpMatrix): print logical NAs "visibly"
850 :     as 'N' (1-letter - Ok?)
851 :    
852 : maechler 1571 * tests/group-methods.R: add test for logical + NAs
853 :    
854 :     * R/dMatrix.R ("Compare"): fix to work with NA's
855 :    
856 :     * R/AllClass.R: "Cholesky" etc now inherit from MatrixFactorization.
857 :    
858 :     * src/lgCMatrix.c (ncsc_to_matrix): renamed from lcsc_to_matrix()
859 :     which is implemented.
860 :    
861 : maechler 1565 2006-09-15 Martin Maechler <maechler@stat.math.ethz.ch>
862 :    
863 : maechler 1571 * src/chm_common.c: coerce logical <-> double instead of
864 :     typecasting; needed for "l" matrix handling in cholmod.
865 : maechler 1565
866 : maechler 1571 * tests/other-pkgs.R (graph): small extension in "graph" checks.
867 :    
868 : maechler 1565 * R/sparseMatrix.R (graphNEL -> Tsparse): method for weight case.
869 :     (Tsp2grNEL): other fixes needed
870 :    
871 : maechler 1548 2006-09-11 Martin Maechler <maechler@stat.math.ethz.ch>
872 :    
873 :     * R/AllClass.R ("nMatrix"): and subclasses for "nonzero pattern"
874 :     Matrices, since "lMatrix", also "lsparseM" can have NA
875 :     * R/ndenseMatrix.R, etc: new source files
876 :     * man/nsparseMatrix-classes.Rd, etc: new help files
877 :     * tests/: adaptions
878 :     * src/chm_common.c (chm_dense_to_SEXP): and others:
879 :     new 'Rkind' argument: "l*" and "d*" both use CHOLMOD_REAL
880 : maechler 1582 * src/Csparse.c, etc: ditto
881 : maechler 1548
882 : bates 1546 2006-09-11 Douglas Bates <bates@R-project.org>
883 :    
884 :     * src/Mutils.[ch],init.c inst/include/*.h: Move the
885 :     alloc_d**Matrix functions to the lme4 package.
886 :    
887 : bates 1543 2006-09-09 Douglas Bates <bates@R-project.org>
888 :    
889 :     * src/dsCMatrix.c (dsCMatrix_Cholesky): igoring LDL = FALSE now
890 : maechler 1544 fixed
891 : bates 1543
892 : maechler 1544 2006-09-09 Martin Maechler <maechler@stat.math.ethz.ch>
893 :    
894 : maechler 1548 * R/lMatrix.R: new
895 :    
896 : maechler 1544 * R/sparseMatrix.R (Tsp2grNEL): do not yet use graph::foo()
897 :    
898 :     * R/dgeMatrix.R: do not define tcrossprod() methods for "matrix"
899 : maechler 1582 * man/tcrossprod.Rd: ditto
900 : maechler 1544
901 : bates 1538 2006-09-08 Douglas Bates <bates@stat.wisc.edu>
902 :    
903 :     * inst/include/Matrix_stubs.c,Matrix.h: Add declarations and stubs
904 :     for exported functions
905 :     * src/Makefile, src/CHOLMOD/Lib/Makefile, src/Metis,CAMD,CCOLAMD:
906 :     Remove partitioning algorithms for sparse matrix reordering. The
907 :     copyright on the Metis code was problematic and the methods were
908 :     rarely used.
909 :     * src/triplet_to_col.[ch],MMHB.[ch]: Remove triplet_to_col. Such
910 :     operations are now done entirely in CHOLMOD code.
911 :    
912 : bates 1517 2006-09-06 Douglas Bates <bates@R-project.org>
913 :    
914 :     * src/Mutils.h: Remove functions that are no longer used.
915 :    
916 : bates 1507 2006-09-04 Douglas Bates <bates@R-project.org>
917 :    
918 :     * src/dtCMatrix.c (dtCMatrix_validate): rename functions.
919 :     * src/DEPS.mkf: update
920 :    
921 : maechler 1481 2006-09-02 Martin Maechler <maechler@stat.math.ethz.ch>
922 :    
923 :     * created branches/Matrix-for-R-2.3.x; on trunk: do
924 :     * DESCRIPTION (Version): 0.9975-0
925 :     (Depends): R (>= 2.4.0)
926 :    
927 : bates 1475 2006-09-01 Douglas Bates <bates@R-project.org>
928 :    
929 :     * R/sparseMatrix.R: Added direct method to CsparseMatrix from graphNEL
930 :    
931 : maechler 1472 2006-09-01 Martin Maechler <maechler@stat.math.ethz.ch>
932 :    
933 :     * R/sparseMatrix.R: add coercion from "ANY" to "sparseMatrix"
934 :     * R/denseMatrix.R: add coercion from "ANY" to "denseMatrix"
935 :    
936 :     * R/Matrix.R ([): use nargs() to disambiguate M[i] and M[i,]
937 :    
938 :     2006-08-31 Martin Maechler <maechler@stat.math.ethz.ch>
939 :    
940 :     * R/sparseMatrix.R (Arith): moved Arith group method one-level up
941 :     from "dsparse" to "sparse" and now go via "Csparse" instead of "dgC"
942 : maechler 1582 * R/dsparseMatrix.R: ditto
943 :     * R/Csparse.R: ditto
944 : maechler 1472
945 :     2006-08-31 Martin Maechler <maechler@stat.math.ethz.ch>
946 :    
947 :     * R/dMatrix.R (Compare): improve availability of "<", etc
948 :     * R/Auxiliaries.R (asTuniq): new; also make use of R 2.4.x print(*,max)
949 :    
950 : maechler 1467 2006-08-30 Martin Maechler <maechler@stat.math.ethz.ch>
951 :    
952 :     * R/dgCMatrix.R: aargh: "Arith(<dgC>, numeric)" was wrong because
953 :     of a 0-index which was used as 1-index (..hmm)
954 :    
955 :     * R/sparseMatrix.R (prSpMatrix): fix printing an all-0 sparse Matrix
956 :    
957 :     * R/Auxiliaries.R (all0, is0): for 0-testing in presence of NA's
958 :     * R/Auxiliaries.R (isTriMat): use all0() for 0-testing.
959 : maechler 1582 (.is.diagonal): ditto
960 : maechler 1467
961 :     * R/lgTMatrix.R: as("matrix", "lgTMatrix"): warn about NA's
962 :    
963 :     * R/Matrix.R (Matrix): also work for NA data
964 :    
965 : maechler 1455 2006-08-28 Martin Maechler <maechler@stat.math.ethz.ch>
966 :    
967 :     * R/Matrix.R (Matrix): + 'forceCheck' argument; dimnames setting
968 :     in all cases.
969 :    
970 : bates 1453 2006-08-27 Douglas Bates <bates@R-project.org>
971 :    
972 :     * src/dense.[ch],init.c, R/ddenseMatrix.R, man/band.Rd
973 :     (ddense_band): Added triu, tril and band for ddenseMatrix objects.
974 :    
975 : maechler 1447 2006-08-25 Martin Maechler <maechler@stat.math.ethz.ch>
976 :    
977 :     * src/Mutils.c (dup_mMatrix_as_dgeMatrix): added all subclasses of
978 :     subclasses of "ddenseMatrix"
979 :     * src/init.c et al: outcomment dtrM*_as_dge* and dsyM*_as_dge*_
980 :     * R/ddenseMatrix.R et al: setAs("ddenseMatrix", "dgeMatrix", ..)
981 :     instead of half dozen specialized ones.
982 :    
983 : bates 1445 2006-08-25 Douglas Bates <bates@R-project.org>
984 :    
985 :     * R/lmer.R (qqmath method): Bug fix provided by Emmanuel Tillard
986 :     <tillard@cirad.fr> - ordering standard errors to match effects.
987 :    
988 : bates 1439 2006-08-24 Douglas Bates <bates@R-project.org>
989 : bates 1431
990 : bates 1439 * src/lsCMatrix.c (lsCMatrix_trans): Remove lsCMatrix_chol based
991 :     on R_ldl.
992 :     * R/lCholCMatrix.R,
993 :     src/[dl]CholCMatrix.[ch],R_ldl.[ch],Metis_utils.[ch]: removed
994 :     * src/dsCMatrix.c (dsCMatrix_to_dgTMatrix): use CHOLMOD
995 :     * many files in ./R and ./src: Use more general version of
996 :     dup_mMatrix_as_dgeMatrix to simplify method definitions.
997 : bates 1442 * src/Mutils.c (dup_mMatrix_as_dgeMatrix): Add ddiMatrix,
998 :     dtpMatrix, dspMatrix and dppMatrix conversions.
999 :    
1000 : maechler 1447
1001 : bates 1439 2006-08-23 Douglas Bates <bates@R-project.org>
1002 :    
1003 :     * R/AllClass.R,lCholCMatrix.R,src/SOURCES_C.mkf,init.c,NAMESPACE:
1004 :     Remove classes lCholCMatrix and dCholCMatrix based on R_ldl code.
1005 : bates 1431 * src/dgeMatrix.c: Ensure 'factors' slot exists in result of
1006 :     dgeMatrix_crossprod (may need to do this in other places).
1007 :     * R/AllGeneric.R,dsCMatrix.R, src/dscMatrix.[ch]: Add Cholesky
1008 :     generic and method for dsCMatrix. Use CHOLMOD for chol().
1009 :    
1010 : bates 1414 2006-08-22 Douglas Bates <bates@R-project.org>
1011 :    
1012 :     * src/Mutils.c (dup_mMatrix_as_dgeMatrix): updated for general
1013 :     types of classed Matrices, matrices or numeric or logical vectors.
1014 : bates 1423 * src/init.c: register dup_mMatrix_as_dgeMatrix for coercions.
1015 :     * src/chm_common.c,Mutils.h (as_cholmod_factor): Move check_class
1016 :     to Mutils.h (as an inline) and change name to Matrix_check_class;
1017 :     fixes in as_cholmod_factor and chm_factor_to_SEXP.
1018 :     * src/dsCMatrix.[ch]: Use CHOLMOD for dsCMatrix_chol and
1019 :     dsCMatrix_matrix_solve. Comment out vestigial functions.
1020 :     * src/Csparse.c: use diag_P and uplo_P macros.
1021 : maechler 1447
1022 : bates 1405 2006-08-21 Douglas Bates <bates@R-project.org>
1023 :    
1024 :     * src/lmer.c (internal_mer_RZXinv): Fix memory leak caught by
1025 : maechler 1447 valgrind.
1026 : bates 1411 * tests/matprod.R: Add tests to verify that 'solve' and '%*%' are
1027 :     inverses.
1028 :     * src/sparseQR.c (sparseQR_validate): add new validation test, fix
1029 :     -Wall warnings.
1030 :     * src/dppMatrix.c,dtrMatrix.c,dgCMatrix.c,dgeMatrix.c,dspMatrix.c:
1031 :     Use dup_mMatrix_as_dgeMatrix.
1032 : maechler 1447
1033 : bates 1403 2006-08-20 Douglas Bates <bates@R-project.org>
1034 :    
1035 :     * src/sparseQR.c: Fix thinko in sparseQR_resid_fitted.
1036 :     * tests/sparseQR.R: Added
1037 :     * man/sparseQR-class.Rd: Document methods for qr.* generics
1038 :     * R/sparseQR.R: Return correct # of coefs; fix cut-and-paste errors
1039 :    
1040 : bates 1398 2006-08-19 Douglas Bates <bates@R-project.org>
1041 :    
1042 :     * NAMESPACE, R/sparseQR.R, src/init.c,sparseQR.[ch],SOURCES_C.mkf:
1043 :     Added methods for sparseQR for qr.qy, qr.qty, qr.coef, qr.resid
1044 :     and qr.fitted.
1045 :     * src/Mutils.[ch]: Added dup_mMatrix_as_dgeMatrix utility
1046 :     * src/dgCMatrix.c: Check for ordering before storing q in dgCMatrix_QR
1047 :    
1048 : maechler 1389 2006-08-18 Martin Maechler <maechler@stat.math.ethz.ch>
1049 :    
1050 :     * R/AllGeneric.R: add "qr" and "chol" generics; via 'trick' since
1051 :     the base version has no "..." argument.
1052 :    
1053 :     * R/sparseMatrix.R (prSpMatrix): fix the triangular unit diagonal case.
1054 :    
1055 :     * R/Matrix.R: define and
1056 :     * NAMESPACE: export as.numeric() and as.logical() methods.
1057 :     Let's hope these do not badly slow down something...
1058 :     Finally export the zapsmall() method.
1059 :    
1060 : bates 1388 2006-08-17 Douglas Bates <bates@R-project.org>
1061 :    
1062 :     * src/dgCMatrix.[ch] (dgCMatrix_matrix_solve), src/init.c,
1063 :     R/dgCMatrix.R: solve methods for dgCMatrix and dense RHS.
1064 :     * src/dtCMatrix.c :Remove code that is no longer used
1065 :     * R/dtCMatrix.R: Use C code for diagU2N in CsparseMatrix classes
1066 :    
1067 : bates 1370 2006-08-14 Douglas Bates <bates@R-project.org>
1068 :    
1069 : bates 1373 * src/Csparse.[ch],init.c (Csparse_to_logical): Added utilities
1070 :     Csparse_to_logical and Csparse_symmetric_to_general.
1071 :     * R/dgCMatrix.R,dsCMatrix.R,Csparse.R : Consolidate general
1072 : maechler 1389 coercion methods between CsparseMatrix and TsparseMatrix.
1073 : bates 1373
1074 :     2006-08-14 Douglas Bates <bates@R-project.org>
1075 :    
1076 : bates 1370 * R/dtCMatrix.R,dgCMatrix.R,Csparse.R src/init.c,dgCMatrix.[ch],
1077 :     Csparse.[ch],chm_common.c,dense.c : Use CHOLMOD code and methods
1078 :     for CsparseMatrix, TsparseMatrix, denseMatrix or matrix when
1079 :     possible.
1080 :    
1081 : bates 1368 2006-08-12 Douglas Bates <bates@R-project.org>
1082 :    
1083 :     * src/chm_common.[ch],Csparse.[ch],Tsparse.[ch],CHMfactor.c,dtTMatrix.c,
1084 :     dgTMatrix.c,dgCMatrix.c,dsCMatrix.c,dtTMatrix.c, R/dsTMatrix.R,
1085 :     Tsparse.R,Csparse.R,dgTMatrix.R,dsCMatrix.R,lsCMatrix.R:
1086 :     generalize conversions between TsparseMatrix, CsparseMatrix,
1087 :     denseMatrix and matrix. Preserve triangularity property and
1088 :     propagate Dimnames in the easy cases.
1089 :    
1090 : bates 1365 2006-08-10 Douglas Bates <bates@R-project.org>
1091 :    
1092 :     * src/lmer.c: adjust checks in glmer_init for S4SXP
1093 :     * tests/validObj.R: check of all(eq) should be all(eq@x) - worked
1094 :     before S4SXP but for the wrong reasons.
1095 :    
1096 : bates 1354 2006-08-08 Douglas Bates <bates@R-project.org>
1097 :    
1098 : bates 1360 * src/Csparse.c (Csparse_crossprod): tcrossprod result has stype = -1.
1099 :     Later modified to return the upper triangle only.
1100 :     * R/dgTMatrix.R: Remove vestigial crossprod and tcrossprod methods.
1101 : maechler 1389
1102 : bates 1352 2006-08-07 Douglas Bates <bates@R-project.org>
1103 :    
1104 :     * src/Csparse.c (Csparse_crossprod): Set stype on result to avoid
1105 :     R-level conversion to a sparse symmetric class.
1106 :     * R/Tsparse.R,R/Csparse.R (crossprod and tcrossprod methods):
1107 :     Remove conversion to sparse symmetric classes (now done in C code).
1108 :    
1109 : maechler 1349 2006-08-07 Martin Maechler <maechler@stat.math.ethz.ch>
1110 :    
1111 : maechler 1351 * R/dgCMatrix.R: disable old crossprod and tcrossprod methods
1112 :     * man/band.Rd: adapt the \dontshow{} unit test.
1113 :    
1114 :     2006-08-07 Martin Maechler <maechler@stat.math.ethz.ch>
1115 :    
1116 : maechler 1349 * DESCRIPTION (Version): 0.995-14 for CRAN
1117 :    
1118 :     * tests/other-pkgs.R: oops: library(Matrix) outside *if* !
1119 :    
1120 :     * R/sparseMatrix.R (Tsp2grNEL): fixed Tsparse -> graph coercion
1121 :     * tests/other-pkgs.R: more checks, sparseMatrix -> graph
1122 :    
1123 :     * R/Auxiliaries.R (as_Tsparse, as_Rsparse): new
1124 :     * R/Tsparse.R (tril, triu, band): methods
1125 : bates 1352 * R/dgRMatrix.R (tril, ...): ditto
1126 :     * man/band.Rd: ditto
1127 : maechler 1349
1128 :     2006-08-04 Martin Maechler <maechler@stat.math.ethz.ch>
1129 :    
1130 :     * R/Matrix.R (head, tail): directly use utils:::head.matrix
1131 :     to be up-to-date automatically.
1132 :    
1133 : maechler 1346 2006-08-03 Martin Maechler <maechler@stat.math.ethz.ch>
1134 :    
1135 :     * DESCRIPTION (Version): 0.995-13 to be released to CRAN
1136 :    
1137 :     * DESCRIPTION (Lazydata): no, instead of 'yes' because it fails for:
1138 :     * data/CAex.R, inst/external/CAex_slots.rda: replacing data/CAex.rda
1139 :     * data/KNex.R, inst/external/KNex_slots.rda: replacing data/KNex.rda
1140 :     such that the S4 objects are always created by the current version
1141 :     of R and 'Matrix' class definitions.
1142 :    
1143 : bates 1342 2006-08-01 Douglas Bates <bates@R-project.org>
1144 :    
1145 :     * R/lmer.R (LMEoptimize method), tests/lmer.R,
1146 : maechler 1346 inst/external/test3comp.rda: Added warnings for convergence on
1147 : bates 1342 boundary and test cases.
1148 :    
1149 :     * src/lmer.c (mer_postVar): Modified to return the variances that
1150 :     are marginal to the fixed effects, not conditional on them (which
1151 :     is what the bVar slot contents represent).
1152 :    
1153 : bates 1338 2006-07-31 Douglas Bates <bates@R-project.org>
1154 :    
1155 :     * NAMESPACE, src/lmer.c, R/lmer.R (hatTrace): Add the hatTrace
1156 :     function which calls the C function mer_hat_trace2.
1157 : maechler 1346
1158 : bates 1342 * man/ranef.Rd: Include description of "postVar" argument and
1159 :     producing a caterpillar plot.
1160 : bates 1338
1161 : maechler 1335 2006-07-31 Martin Maechler <maechler@stat.math.ethz.ch>
1162 :    
1163 :     * NAMESPACE: change "correlation" to "corMatrix"
1164 :     * R/AllClass.R: to avoid clash with S3 class in 'nlme'.
1165 : bates 1352 * R/dpoMatrix.R: ditto
1166 :     * R/lmer.R: ditto
1167 : maechler 1335
1168 : bates 1338 2006-07-28 Douglas Bates <bates@R-project.org>
1169 :    
1170 :     * src/lmer.c (internal_mer_RZXinv): Split the calculation of the
1171 :     RZXinv slot's contents into a separate internal function that can
1172 :     be used in mer_hat_trace.
1173 :    
1174 : maechler 1331 2006-07-22 Martin Maechler <maechler@stat.math.ethz.ch>
1175 :    
1176 :     * R/Matrix.R: Coercions "Matrix" -> (sparse|dense)Matrix
1177 :     via new smart
1178 :     * R/Auxiliaries.R (as_Csparse, as_dense, .M.shapse): new
1179 :     utility functions.
1180 :    
1181 :    
1182 : maechler 1330 2006-07-21 Martin Maechler <maechler@stat.math.ethz.ch>
1183 :    
1184 : maechler 1331 * R/Csparse.R (tril, triu, band): do return *triangular* classed
1185 :     matrices when appropriate; band() even symmetric ones.
1186 :     (replCmat): extend to potentially all "CsparseMatrix"
1187 :     * R/Tsparse.R (replTmat): extend to all "TsparseMatrix"; hence
1188 :     allow subassignment for special sparse matrices.
1189 :    
1190 :     * R/Auxiliaries.R (as_geClass): factor out the .M.kind() functionality
1191 :    
1192 : maechler 1330 * src/lmer.c (mer_MCMCsamp, glmer_MCMCsamp): new 'verbose'
1193 :     argument; in glmer_*(): print only if(verbose).
1194 :    
1195 :     speed-optimize a few places by moving REAL(.) out of loops.
1196 :    
1197 :     * src/lmer.h, src/init.h, R/lmer.R: related to above.
1198 :    
1199 : maechler 1329 2006-07-20 Martin Maechler <maechler@stat.math.ethz.ch>
1200 :    
1201 :     * R/Matrix.R("["): disable ("Matrix", i = "logical", j = "missing"),
1202 :     since that wrongly triggers also for M[ logi , ]
1203 :    
1204 :     * R/denseMatrix.R: "[" methods now also work e.g. when indexing
1205 :     a symmetric matrix that results in a non-symmetric one.
1206 :     * R/Auxiliaries.R (as_geClass): new function used in "[" above.
1207 :    
1208 :     * R/dMatrix.R: make round(M) work as round(M, 0)
1209 :    
1210 :     * R/dgTMatrix.R (image): coordinate system and axis now use
1211 :     1-based indices, not 0-based ones.
1212 :    
1213 :     * R/Tsparse.R (.ind.prep for "["): get rid of max(<empty>) warning.
1214 :     * tests/indexing.R: test it.
1215 :    
1216 :     * NAMESPACE: export isSymmetric(); has been a generic in "base" for a while;
1217 :     * man/isSymmetric-methods.Rd: and document it.
1218 :    
1219 :     * R/SparseM-conv.R: added coercion methods for some 'SparseM' matrices.
1220 :     * man/SparseM-conv.Rd: docu them
1221 :    
1222 :     * tests/other-pkgs.R: renamed from tests/graph.R and add example
1223 :     for 'SparseM' conversions
1224 :    
1225 :     2006-07-17 Douglas Bates <Douglas.Bates@R-project.org>
1226 :    
1227 :     * R/Matrix.R (head): added head() and tail() methods.
1228 :    
1229 :     2006-07-17 Martin Maechler <maechler@stat.math.ethz.ch>
1230 :    
1231 :     * DESCRIPTION (Version): 0.995-12 released to CRAN
1232 :    
1233 : maechler 1319 2006-07-15 Martin Maechler <maechler@stat.math.ethz.ch>
1234 :    
1235 :     * tests/simple.R: add check for correct dsT -> dgT coercion;
1236 :     add check for correct printing of symmetric sparse matrices.
1237 :    
1238 :     * R/Auxiliaries.R (non0ind): return *all* non-0 entry indices also
1239 :     for sparse symmetric matrices.
1240 :    
1241 :     * src/dsTMatrix.c (dsTMatrix_as_dgTMatrix): do not copy the
1242 :     diagonal twice.
1243 :    
1244 : bates 1316 2006-07-11 Douglas Bates <Douglas.Bates@R-project.org>
1245 :    
1246 :     * src/dsTMatrix.c (dsTMatrix_as_dgTMatrix): Fix a case of INTEGER
1247 : maechler 1319 being applied to the x slot (detected by Brian Ripley).
1248 : bates 1316
1249 : maechler 1315 2006-07-10 Martin Maechler <maechler@stat.math.ethz.ch>
1250 :    
1251 :     * src/dgCMatrix.c (dgCMatrix_validate): 'p' slot must have correct length.
1252 :    
1253 :     * R/Auxiliaries.R (isTriC): fix buglet (we were 1-based!)
1254 :    
1255 :     2006-07-08 Martin Maechler <maechler@stat.math.ethz.ch>
1256 :    
1257 :     * src/lgCMatrix.c (lgCMatrix_diag): new function
1258 :     * R/lgCMatrix.R (diag): for new method
1259 :    
1260 :     * R/AllClass.R (TsparseMatrix): do use Tsparse_validate
1261 :     ==> construction of illegal "*gTMatrix" via new() should
1262 :     now be much less easy:
1263 :     * tests/Class+Meth.R: assertError() for some illegal "dgT*"
1264 :    
1265 :     * R/Matrix.R (Matrix): Matrix(0, nrow,ncol) now "goes sparse"
1266 :     directly.
1267 :     * man/Matrix.Rd: documents it.
1268 :    
1269 : bates 1311 2006-07-06 Douglas Bates <bates@R-project.org>
1270 :    
1271 :     * src/pedigree.c (pedigree_inbreeding): Correction in
1272 :     initialization. This function is not currently being used and is
1273 :     not fully tested.
1274 :    
1275 : bates 1312 * NAMESPACE, R/{AllClass.R,lmer.R}, src/{init.c,lmer.c}:
1276 :     Introduced the glmer class. Added code for mcmcmsamp on glmer
1277 :     objects. Modified validity check on pedigree objects to account
1278 :     for nonparallel patterns of missingness of parents.
1279 : bates 1311
1280 : bates 1313 * man/{lmer-class.Rd,mcmcsamp.Rd}: Update documentation for glmer
1281 :     class.
1282 : maechler 1315
1283 :     2006-07-01 Martin Maechler <maechler@stat.math.ethz.ch>
1284 :    
1285 :     * R/pMatrix.R: coercion pMatrix -> Tsparse
1286 :    
1287 : bates 1300 2006-06-12 Douglas Bates <bates@R-project.org>
1288 :    
1289 : maechler 1319 * DESCRIPTION (Version): 0.995-11 released to CRAN
1290 :    
1291 : bates 1300 * R/lmer.R (mcmcsamp method): Corrected arrangments of names on
1292 :     the output from mcmcsamp.
1293 :    
1294 : bates 1298 2006-06-10 Douglas Bates <bates@R-project.org>
1295 :    
1296 : bates 1300 * R/lmer.R (simulestimate): added C code for calculating the trace
1297 :     of the hat matrix.
1298 : bates 1298
1299 : maechler 1295 2006-06-09 Martin Maechler <maechler@stat.math.ethz.ch>
1300 :    
1301 :     * R/diagMatrix.R (setAs): define coercion methods to sparse matrix
1302 :     classes.
1303 : maechler 1315 * R/sparseMatrix.R etc: multiplication of diagonal and sparse
1304 : maechler 1295
1305 : maechler 1290 2006-06-08 Martin Maechler <maechler@stat.math.ethz.ch>
1306 :    
1307 :     * R/dgTMatrix.R (colSums): etc. All four of
1308 :     colSums(), rowSums(), colMeans(), rowMeans() now should work for
1309 :     all "Matrices".
1310 :    
1311 : bates 1288 2006-06-01 Douglas Bates <bates@stat.wisc.edu>
1312 :    
1313 :     * R/lmer.R (panel.ci): Add a reference line at zero and a
1314 :     background grid to the qqmath plot of ranef.lmer.
1315 :    
1316 : bates 1287 2006-05-30 Douglas Bates <bates@stat.wisc.edu>
1317 : bates 1284
1318 : bates 1287 * R/lmer.R (expandSlash): Functions (non-exported) to allow nested
1319 :     grouping factors to be specified in the formula as (1|foo/bar).
1320 :    
1321 :     2006-05-27 Douglas Bates <bates@stat.wisc.edu>
1322 :    
1323 : bates 1284 * R/lmer.R (findbars and others): Change check of is.numeric to
1324 :     !is.language to resolve the bug reported by Jacob Wegelin.
1325 :    
1326 :     * src/pedigree.c (pedigree_inbreeding): Initial implementation of
1327 :     code to evaluate inbreeding coefficients without calculating T,
1328 :     based on code in Sargolzaei and Iwaisaki's paper.
1329 :    
1330 : bates 1283 2006-05-27 Douglas Bates <bates@stat.wisc.edu>
1331 :    
1332 :     * R/{lmer.R,AllGeneric.R}, src/{init.c,lmer.[ch]}: Added local
1333 :     generic and mer methods for isNested and denomDF. This denomDF was
1334 :     an attempt to emulate that in lme but I don't think that makes
1335 :     sense. Use the trace of the hat matrix instead.
1336 :    
1337 : maechler 1271 2006-05-17 Martin Maechler <maechler@stat.math.ethz.ch>
1338 :    
1339 :     * R/sparseMatrix.R: Matrix <-> graph methods: can no longer use
1340 :     the C code depending on a slot structure that's no longer valid.
1341 : bates 1352 * src/dgTMatrix.c: ditto (also: src/init.c src/dgTMatrix.h)
1342 : maechler 1271
1343 :    
1344 : bates 1268 2006-05-17 Douglas Bates <bates@stat.wisc.edu>
1345 :    
1346 :     * R/{AllGeneric.R,Csparse.R},man/band.Rd,NAMESPACE: changed name
1347 :     of lowerTriMatrix generic and methods to tril (also upper to triu)
1348 :     and added a general band extractor.
1349 :    
1350 : bates 1267 2006-05-16 Douglas Bates <bates@stat.wisc.edu>
1351 :    
1352 :     * R/pedigree.R (pedigree): Replace sire and dam values outside the
1353 :     allowable range with NAs. Added a corresponding check in the
1354 :     validity check for the pedigree class.
1355 :    
1356 :     * R/[CT]sparse.R ([t]crossprod): The result of single-argument
1357 :     crossprod methods now inherits from symmetricMatrix.
1358 :    
1359 : bates 1265 2006-05-15 Douglas Bates <bates@stat.wisc.edu>
1360 :    
1361 :     * R/AllGeneric.R (lowerTriMatrix): Added (but did not export)
1362 :     generics lowerTriMatrix and upperTriMatrix along with methods for
1363 :     the Csparse virtual class. Also added a C function Csparse_band
1364 :     that implements these methods by calling cholmod_band.
1365 :    
1366 : maechler 1264 2006-05-15 Martin Maechler <maechler@stat.math.ethz.ch>
1367 :    
1368 :     * R/Tsparse.R ("["): column or row subsetting; @Dimnames[k] got
1369 :     erased when it was NULL. This led to invalid subselections!
1370 :    
1371 : bates 1259 2006-04-25 Douglas Bates <bates@stat.wisc.edu>
1372 :    
1373 :     * R/dtCMatrix.R: avoid coercion of dtCMatrix object to dgCMatrix
1374 :     in method for "t" so as not to lose the unit diagonal property.
1375 :    
1376 : bates 1257 2006-04-19 Douglas Bates <bates@stat.wisc.edu>
1377 :    
1378 :     * R/lmer.R, R/AllGeneric.R, NAMESPACE: Remove the postVar generic
1379 :     and methods. This is now an option to the ranef method for the
1380 :     mer class.
1381 :    
1382 :     * src/cs_utils.c: Ensure that the nz component is -1 for a
1383 :     compressed column-oriented matrix. Minor formatting cleanup.
1384 :    
1385 :     * man/lmer-class.Rd: Document the qqmath method for ranef.lmer
1386 :     objects.
1387 :    
1388 : maechler 1253 2006-04-19 Martin Maechler <maechler@stat.math.ethz.ch>
1389 :    
1390 :     * R/Auxiliaries.R (diagU2N): new for the solve() methods in
1391 :     * R/dtCMatrix.R: where dgC -> dgT coercion now preserves diag = "U".
1392 :    
1393 : bates 1251 2006-04-15 Douglas Bates <bates@stat.wisc.edu>
1394 :    
1395 :     * src/cs.[ch],src/cs_utils.[ch] : Added Tim Davis' CSparse library
1396 :     in cs.[ch] and utilities to interface to that code in cs_utils.[ch].
1397 :    
1398 :     * R/dtCMatrix.R, src/dtCMatrix.[ch] : CSparse-based solve methods
1399 :     for the dtCMatrix class.
1400 : maechler 1253
1401 : bates 1247 2006-04-12 Douglas Bates <bates@stat.wisc.edu>
1402 :    
1403 :     * R/pedigree.R, R/AllClass.R, NAMESPACE: added a pedigree class
1404 :     and methods for it.
1405 :    
1406 : maechler 1245 2006-04-12 Martin Maechler <maechler@stat.math.ethz.ch>
1407 :    
1408 :     * R/dgCMatrix.R: add storage.mode(.) <- "double" for "matrix"
1409 :     arguments, such that M %*% 1:6 now works
1410 :     * Tests/matprod.R: test the above
1411 :    
1412 : bates 1244 2006-04-03 Douglas Bates <bates@stat.wisc.edu>
1413 : bates 1243
1414 :     * R/lmer.R (qqmath,ranef.lmer-method): added a qqmath method for
1415 :     the ranef.lmer class.
1416 :    
1417 :     * R/AllClass.R, NAMESPACE, R/lmer.R: Added a postVar generic and
1418 :     methods to extract the posterior variances from the bVar slot.
1419 :    
1420 : maechler 1238 2006-03-30 Martin Maechler <maechler@stat.math.ethz.ch>
1421 :    
1422 :     * R/dtCMatrix.R: allow coercion from dgC* to triangular (dtC*)
1423 :     * R/dsCMatrix.R: and symmetric (dsC*) 'Csparse' matrices.
1424 :    
1425 :     * R/Tsparse.R: Tsparse* -> Csparse* coercion now works and is tested in
1426 :     * tests/simple: (extended)
1427 :    
1428 :     * R/sparseMatrix.R (isTriangular): now using much improved
1429 :     * R/Auxiliaries.R (isTriC): new triangularity check for *CMatrix
1430 :    
1431 : bates 1236 2006-03-23 Douglas Bates <bates@stat.wisc.edu>
1432 :    
1433 :     * src/dsyMatrix.c (dsyMatrix_as_dspMatrix): Propagate DimNames
1434 :     (problem report from Franklin Parlamis). This should be done
1435 : maechler 1238 generally.
1436 : bates 1236
1437 : bates 1234 2006-03-21 Douglas Bates <bates@stat.wisc.edu>
1438 :    
1439 :     * R/AllClass.R,lmer.R: Change the name of the lmer.ranef class to
1440 :     ranef.lmer (like summary.lmer). Add the coef.lmer class and
1441 :     update the plot methods.
1442 :    
1443 : bates 1232 2006-03-20 Douglas Bates <bates@stat.wisc.edu>
1444 :    
1445 :     * R/lmer.R (resid and ranef methods): Added methods for the
1446 :     "residuals" and "resid" generic but only for linear mixed model
1447 :     fits. Changed the ranef method to return a list of data frames so
1448 :     that the plot methods now work.
1449 :    
1450 : bates 1230 2006-03-16 Douglas Bates <bates@bates2>
1451 :    
1452 :     * src/dpoMatrix.c (dpoMatrix_chol): Require n > 0 in call to
1453 :     dpotrf - otherwise the BLAS on Mac OS X complains and quits.
1454 :    
1455 :     * DESCRIPTION (Date): New release
1456 :    
1457 : maechler 1228 2006-03-15 Martin Maechler <maechler@stat.math.ethz.ch>
1458 :    
1459 :     * DESCRIPTION (Version): 0.995-6 -- to be released to CRAN
1460 :    
1461 :     * data/KNex.rda: replacing 'mm' and 'y' by KNex <- list(mm=mm, y=y)
1462 :     * man/KNex.Rd: and other help files
1463 :     * tests/*.R: several ones needed adaption
1464 : bates 1352 * inst/doc/Comparisons.Rnw: ditto
1465 : maechler 1228
1466 : maechler 1226 2006-03-11 Martin Maechler <maechler@stat.math.ethz.ch>
1467 :    
1468 :     * R/dgCMatrix.R (replCmat): "[<-" methods for dgCMatrix
1469 :    
1470 :     * tests/indexing.R: tests for new [<- methods for sparse matrices.
1471 :    
1472 :     2006-03-10 Martin Maechler <maechler@stat.math.ethz.ch>
1473 :    
1474 :     * R/dgTMatrix.R (replTmat): "[<-" methods for dgTMatrix
1475 :    
1476 :     * R/Tsparse.R (.ind.prep): fix out-of-range indexing
1477 :    
1478 :     2006-03-08 Martin Maechler <maechler@stat.math.ethz.ch>
1479 :    
1480 :     * R/dMatrix.R: enable things like M [ M < 10 ]
1481 :     * R/dgeMatrix.R: implement it
1482 :    
1483 : maechler 1222 2006-03-06 Martin Maechler <maechler@stat.math.ethz.ch>
1484 :    
1485 :     * R/AllClass.R: define "summary.mer" and "*.lmer"
1486 :     * R/lmer.R (summary): summary(<mer>) computes & returns the above;
1487 :     * R/lmer.R (show): now works with summary()
1488 :    
1489 :     2006-03-04 Martin Maechler <maechler@stat.math.ethz.ch>
1490 :    
1491 :     * R/dgCMatrix.R: finally direct "Arith" dgC o dgC
1492 :     * R/Auxiliaries.R (WhichintersectInd): and other utilities to
1493 :     support the above
1494 :    
1495 : bates 1213 2006-02-07 Douglas Bates <bates@stat.wisc.edu>
1496 :    
1497 :     * R/lmer.R (lmer): fix initial values of offset and weights for glm.fit.
1498 :     Use glmFit$prior.weights for weights in a glmm.
1499 :     Allow an option usePQL = FALSE to skip the PQL steps for the
1500 :     Laplace method (and, in time, the AGQ method).
1501 :    
1502 :     * src/lmer.c (mer_factor): Move downdating and factoring of XtX
1503 :     into a separate function internal_mer_Xfactor to be able to call
1504 :     it from internal_bhat.
1505 :    
1506 : maechler 1200 2006-01-23 Martin Maechler <maechler@stat.math.ethz.ch>
1507 :    
1508 :     * tests/Class+Meth.R (tstMatrixClass): function for much better
1509 :     testing; now again of all actual classes.
1510 :    
1511 :     * src/Mutils.c (MAKE_TRIANGULAR_BODY, MAKE_SYMMETRIC_BODY):
1512 :     use macros and define make_d_matrix_* and make_i_matrix_*
1513 :     where _i_ is for the ldense routines:
1514 :    
1515 :     * src/ldense.c (ltrMatrix_as_lgeMatrix): provide functions
1516 :     * src/ldense.c (lsyMatrix_as_lgeMatrix):
1517 :    
1518 :     * R/ldenseMatrix.R: use the above in setAs(*,"lgeMatrix")
1519 :    
1520 :    
1521 : maechler 1174 2006-01-16 Martin Maechler <maechler@stat.math.ethz.ch>
1522 :    
1523 :     * R/Matrix.R (Matrix): has become much "smarter" now auto-producing
1524 :     many different kinds of matrices.
1525 :     * R/*.R: quite a few new methods were needed for R CMD check with
1526 :     new Matrix(). Very good for users playing around.
1527 :    
1528 :    
1529 : maechler 1165 2006-01-15 Martin Maechler <maechler@stat.math.ethz.ch>
1530 :    
1531 :     * src/dgeMatrix.c (dMatrix_validate): new
1532 :     * src/Mutils.c (dense_nonpacked_validate): new
1533 :    
1534 :     * src/dtrMatrix.c (dtrMatrix_validate): improved/fixed
1535 :    
1536 :    
1537 :     2006-01-14 Douglas Bates <bates@stat.wisc.edu>
1538 :    
1539 :     * R/AllClass.R (compMatrix), (generalMatrix): new virtual classes
1540 :    
1541 : bates 1123 2006-01-07 Douglas Bates <bates@stat.wisc.edu>
1542 : bates 1119
1543 : maechler 1127 * DESCRIPTION (Version): 0.99-6 released to CRAN
1544 :    
1545 : bates 1119 * src/dgBCMatrix.c (cscb_trcbsm): Fix due to Peter Dalgaard for
1546 :     segfault in cases with multiple non-nested grouping factors.
1547 :    
1548 : maechler 1109 2006-01-03 Martin Maechler <maechler@stat.math.ethz.ch>
1549 :    
1550 :     * DESCRIPTION (Version): 0.99-4 to be released to CRAN
1551 :     (Depends): also on 'utils'
1552 :    
1553 :     * R/AllClass.R (diagonalMatrix): new class with "ddi*" and "ldi*"
1554 :     * R/diagMatrix.R (Diagonal): constructor and methods for
1555 :     diagonal matrices
1556 :    
1557 :     * R/ltTMatrix.R: new "minimal methods"
1558 :    
1559 : maechler 1091 2005-12-12 Martin Maechler <maechler@stat.math.ethz.ch>
1560 :    
1561 :     * R/AllGeneric.R (tcrossprod): 2-argument version; here, and for
1562 :     all methods (and help files).
1563 :    
1564 : maechler 1084 2005-12-09 Martin Maechler <maechler@stat.math.ethz.ch>
1565 :    
1566 :     * R/Auxiliaries.R (dimNamesCheck): fixed thinko -> bug
1567 :     for case (dimn. op no_dimn.)
1568 :    
1569 :     2005-11-14 Douglas Bates <bates@stat.wisc.edu>
1570 :    
1571 : maechler 1174 * DESCRIPTION (Version): 0.99-2 released to CRAN
1572 : maechler 1084
1573 : bates 988 2005-10-21 Douglas Bates <bates@stat.wisc.edu>
1574 :    
1575 :     * R/lmer.R (simulate method): Fixed a drop=FALSE problem reported
1576 :     by Julian Faraway.
1577 :    
1578 : maechler 976 2005-10-06 Martin Maechler <maechler@stat.math.ethz.ch>
1579 :    
1580 :     * R/Auxiliaries.R (try_as): new utility
1581 :     * R/sparseMatrix.R: use try_as() in coercion to original class
1582 :    
1583 : maechler 956 2005-09-30 Martin Maechler <maechler@stat.math.ethz.ch>
1584 :    
1585 :     * src/dgCMatrix.c (double_to_csc): and dgeMatrix_to_csc()
1586 :    
1587 :     2005-09-29 Martin Maechler <maechler@stat.math.ethz.ch>
1588 :    
1589 :     * R/Auxiliaries.R (dimNamesCheck): added
1590 :    
1591 :     * R/Matrix.R (as.array), (as.vector): new
1592 :    
1593 : maechler 954 2005-09-28 Martin Maechler <maechler@stat.math.ethz.ch>
1594 :    
1595 :     * R/Matrix.R (Matrix): get logical argument 'sparse' with a smart
1596 : maechler 956 default.
1597 :     * R/AllClass.R: move 'factors' slot toplevel "Matrix";
1598 :     "pMatrix" now contains "sparseMatrix"
1599 : maechler 954
1600 : maechler 948 2005-09-26 Martin Maechler <maechler@stat.math.ethz.ch>
1601 :    
1602 :     * tests/Class+Meth.R: new tests; t(t(m)) == m
1603 :    
1604 :     * src/dtCMatrix.c (tsc_transpose): add forgotten "diag" slot
1605 :    
1606 :     * src/dsTMatrix.c (dsTMatrix_as_dsCMatrix): bad typo (segfault!)
1607 :     * src/dtTMatrix.c (dtTMatrix_as_dtCMatrix): new
1608 :    
1609 :     * R/dspMatrix.R: typo in "t" method
1610 :    
1611 : maechler 925 2005-09-18 Douglas Bates <bates@wisc.edu>
1612 :    
1613 :     * R/AllClass.R (TsparseMatrix), CsparseM* and RsparseM*
1614 :     * R/Tsparse.R: instead of R/gTMatrix.R
1615 :     * R/Csparse.R: new
1616 :     * src/Tsparse.c (Tsparse_to_Csparse): new; -> cholmod_()
1617 :     * src/Tsparse.c: new; many trivial methods calling cholmod_()
1618 :     * src/Csparse.c (Csparse_to_Tsparse), transpose, (mat|cross)prod:
1619 :     via cholmod
1620 :    
1621 :     2005-09-16 Martin Maechler <maechler@stat.math.ethz.ch>
1622 :    
1623 :     * R/Auxiliaries.R (non0ind): new function using new C code
1624 :     * src/dgCMatrix.c (compressed_non_0_ij): new utility
1625 :    
1626 : bates 917 2005-09-15 Douglas Bates <bates@localhost.localdomain>
1627 :    
1628 :     * src/chm_common.h: header file required by all C sources that
1629 : maechler 1174 call CHOLMOD functions. It defines a cholmod_common structure
1630 : bates 917 called 'c' whose address is passed as the last argument to
1631 :     (virtually) every CHOLMOD function.
1632 :    
1633 :     * src/Pattern.c: Simple example of the use of CHOLMOD.
1634 :    
1635 :     * src/init.c: initialize and finalize the cholmod_common structure.
1636 :    
1637 :     * src/Makefile: Added source packages CHOLMOD UMFPACK AMD COLAMD
1638 :     LDL and CCOLAMD from the U. of Florida sparse matrix library.
1639 :    
1640 : maechler 908 2005-09-08 Martin Maechler <maechler@stat.math.ethz.ch>
1641 :    
1642 :     * inst/test-tools.R: new file collecting the utility functions used
1643 :     in ./tests/*.R
1644 :    
1645 :     * R/ddenseMatrix.R (cbind2): new methods for "numeric" and "matrix"
1646 :     * R/Matrix.R (cbind2): methods for NULL and missing
1647 :    
1648 : maechler 886 2005-08-31 Martin Maechler <maechler@stat.math.ethz.ch>
1649 :    
1650 :     * R/AllClass.R: new "index" class for "[" and "[<-":
1651 :     First cut at "symmetricMatrix" and "triangularMatrix"
1652 :     * R/gTMatrix.R (.ind.prep): new function;
1653 : maechler 1174 Logical and character indexing now work too.
1654 : maechler 886 * R/Matrix.R: cheap "[<-" methods for denseMatrix now work
1655 :     * tests/indexing.R: new, including *.Rout.save
1656 :     * tests/dgTMatrix.R: new
1657 :    
1658 : bates 876 2005-08-29 Douglas Bates <bates@wisc.edu>
1659 :    
1660 :     * src/dgTMatrix.c (graphNEL_as_dgTMatrix): Corrected the position
1661 :     indicator pos not being updated. Also enforced upper triangular
1662 :     for symmetric case. Need to coerce edges component of elements of
1663 :     edge list - grr! (Why don't they define their classes cleanly?)
1664 :    
1665 : maechler 871 2005-08-26 Martin Maechler <maechler@stat.math.ethz.ch>
1666 :    
1667 :     * R/Matrix.R: added first "[<-" methods; not yet functional
1668 : bates 1352 * R/denseMatrix.R: ditto
1669 : maechler 871 * man/Subassign-methods.Rd: new help file for these
1670 :    
1671 :     2005-08-25 Martin Maechler <maechler@stat.math.ethz.ch>
1672 :    
1673 :     * DESCRIPTION (Version): 0.98-6
1674 :    
1675 :     * R/denseMatrix.R: new file for "[" fallback methods for all dense
1676 :     matrices.
1677 :    
1678 : maechler 868 2005-08-19 Martin Maechler <maechler@stat.math.ethz.ch>
1679 :    
1680 :     * src/lgCMatrix.c (lcsc_to_matrix): new; need for
1681 :     as( <logical>, "matrix")
1682 :    
1683 :     * R/pMatrix.R: coercion to "lgTMatrix"
1684 :    
1685 :     * R/gTMatrix.R: new virtual class to define "[" methods for.
1686 :     * man/gTMatrix-class.Rd:
1687 :     * General slight re-organization of where "[" methods are defined.
1688 :     more to come.
1689 :    
1690 : maechler 871 2005-08-18 Douglas Bates <bates@wisc.edu>
1691 : maechler 868
1692 : maechler 1174 * DESCRIPTION (Version): 0.98-5 released to CRAN
1693 : maechler 871
1694 :     * src/dgTMatrix.c (graphNEL_as_dgTMatrix): add first graphNEL methods
1695 :     * .....
1696 :    
1697 : bates 863 2005-08-18 Douglas Bates <bates@localhost.localdomain>
1698 :    
1699 :     * R/lmer.R: Corrected naming scheme in mcmcsamp to work with lmer
1700 :     or glmer objects.
1701 :    
1702 : maechler 860 2005-08-17 Martin Maechler <maechler@stat.math.ethz.ch>
1703 :    
1704 :     * DESCRIPTION (Version): 0.98-4 : upload to CRAN
1705 :    
1706 :     2005-08-16 Douglas Bates <bates@localhost.localdomain>
1707 :    
1708 :     * R/HBMM.R: finish re-writing R-only code.
1709 :    
1710 : bates 854 2005-08-15 Douglas Bates <bates@localhost.localdomain>
1711 :    
1712 :     * man/externalFormats.Rd: move documentation for writeHB and
1713 :     writeMM here.
1714 :    
1715 :     * src/mmio.c: replace inclusion of <malloc.h> by <stdlib.h>
1716 :     (suggested by Paul Roecker).
1717 :    
1718 :     * tests/validObj.R (assertError): Comment out test that is failing
1719 :     after recent changes in r-devel.
1720 :    
1721 : maechler 860
1722 : maechler 848 2005-08-11 Martin Maechler <maechler@stat.math.ethz.ch>
1723 :    
1724 :     * R/AllClass.R: intermediate virtual class "denseMatrix"
1725 :     * man/denseMatrix-class.Rd
1726 :     * NAMESPACE: export it, and also export
1727 :     * man/unused-classes.Rd: "iMatrix", "zMatrix" and "ldenseMatrix"
1728 :    
1729 : bates 846 2005-08-10 Douglas Bates <bates@wisc.edu>
1730 :    
1731 : maechler 848 * DESCRIPTION (Version): 0.98-3 to CRAN
1732 :    
1733 : bates 846 * src/dtrMatrix.c (dtrMatrix_validate): fixed up validation and
1734 :     matrix_solve code (which was really, really wrong).
1735 :    
1736 : bates 835 2005-08-07 Douglas Bates <bates@wisc.edu>
1737 : maechler 834
1738 :     * DESCRIPTION (Version): 0.98-2
1739 :    
1740 :     * R/HBMM.R (readHB), (readMM): read Matrix Market formats
1741 :    
1742 :     * R/lmer.R (abbrvNms): new
1743 :     * R/lmer.R (mcmcsamp): allow transformed parameters
1744 : bates 835 * src/HBMM.c (Matrix_writeMatrixMarket): Added read/write routines
1745 :     for the Harwell-Boeing and the MatrixMarket formats.
1746 : maechler 834
1747 :     2005-08-04 Martin Maechler <maechler@stat.math.ethz.ch>
1748 :    
1749 :     * man/dtrMatrix-class.Rd: add examples
1750 : bates 835 * man/dtpMatrix-class.Rd: ditto; plus note about PROBLEM
1751 : maechler 834
1752 :     * TODO: note the dtpMatrix (docu) bug
1753 :    
1754 :     * R/zzz.R (.onLoad): assignInNamespace("as.matrix", *, "base")
1755 :     in order to ensure that new as.matrix() is used by old functions,
1756 :     e.g., svd(), qr(), eigen(), dist(),..;
1757 :     apply(), also matplot() or pairs().
1758 :    
1759 :    
1760 :     2005-08-03 Martin Maechler <maechler@stat.math.ethz.ch>
1761 :    
1762 :     * R/lmer.R: add 'fixme' comments and move the linear vs glm check;
1763 :     add comments about 'control' / lmerControl() arguments
1764 :    
1765 : bates 835 2005-07-27 Douglas Bates <bates@wisc.edu>
1766 : bates 820
1767 : bates 835 * man/sleepstudy.Rd: Added the sleep data set.
1768 : maechler 1174 * DESCRIPTION (Version): 0.98-1 released to CRAN
1769 : bates 820
1770 : bates 835 2005-07-12 Douglas Bates <bates@wisc.edu>
1771 : maechler 834 * man/sleepstudy.Rd: Added the sleep data set.
1772 :    
1773 : bates 809 * R/lmer.R (glmmMCMC): Added PACKAGE = "Matrix" in a couple of
1774 :     .Call calls that were producing spurious output.
1775 :    
1776 : bates 835 2005-07-05 Douglas Bates <bates@wisc.edu>
1777 : bates 801
1778 :     * R/lmer.R (lmer): stored updated variance component estimates in
1779 :     mer object for the generalized model. (Bug reported by Renaud
1780 :     Lancelot).
1781 :    
1782 : bates 835 2005-07-03 Douglas Bates <bates@wisc.edu>
1783 : bates 794
1784 :     * src/lmer.c (glmer_devAGQ): Added AGQ for single grouping factor,
1785 :     unidimensional case.
1786 :    
1787 : bates 835 2005-06-08 Douglas Bates <bates@wisc.edu>
1788 : maechler 791
1789 :     * DESCRIPTION (Version): 0.96-1
1790 :    
1791 : maechler 1174 * moved lmer-class' R and C code moved from lme4 to here
1792 : maechler 791
1793 : bates 835 2005-06-04 Douglas Bates <bates@wisc.edu>
1794 : bates 763
1795 :     * R/dgCMatrix.R: Call to csc_matrix_mm used undefined arguments
1796 :     (reported by Guissepe Ragusa <gragusa@ucsd.edu>)
1797 :    
1798 : bates 835 2005-06-02 Douglas Bates <bates@wisc.edu>
1799 : bates 763
1800 :     * src/Makefile.win: Forgot to update this when Makefile changed.
1801 :    
1802 : bates 835 2005-05-11 Douglas Bates <bates@wisc.edu>
1803 : bates 726
1804 :     * src/dgCMatrix.c (csc_transpose): Simplified function fixing a
1805 :     bug reported by Kurt Hornik and Michael Hahsler.
1806 :    
1807 : bates 835 2005-05-10 Douglas Bates <bates@wisc.edu>
1808 : bates 725
1809 :     * src/lgCMatrix.c (Matrix_lgClgCmm): Implementation of methods for
1810 :     logical sparse matrices. These will also be used in the symbolic
1811 :     analysis for lmer objects.
1812 :    
1813 :     * src/dsCMatrix.c (dsCMatrix_matrix_solve): Copied the dimensions
1814 :     of b to the result. Fixes bug reported by Jean.Coursol@math.u-psud.fr
1815 : maechler 791
1816 : bates 835 2005-05-06 Douglas Bates <bates@wisc.edu>
1817 : bates 714
1818 :     * src/dgeMatrix.c (dgeMatrix_colsums): Added an implementation of
1819 :     colMeans, colSums, rowMeans and rowSums.
1820 :    
1821 : bates 835 2005-04-18 Douglas Bates <bates@wisc.edu>
1822 : bates 692
1823 :     * src/lgCMatrix.[ch]: code for _validate method and stub for
1824 :     multiplication operation.
1825 :    
1826 :     * src/dgeMatrix.c (dgeMatrix_matrix_solve): Passing wrong argument
1827 :     to dgetrs.
1828 :    
1829 :     * src/init.c: Fix cut-and-paste error in definition of
1830 :     dgeMatrix_matrix_solve
1831 :    
1832 :     * src/{many files}: Tighten code by using ALLOC_SLOT.
1833 :    
1834 : bates 835 2005-04-15 Douglas Bates <bates@wisc.edu>
1835 : bates 692
1836 :     * R/AllClass.R: Add lgTMatrix and lgCMatrix classes
1837 :    
1838 :     * DESCRIPTION: Eliminate import of stats.
1839 :    
1840 : maechler 791
1841 : bates 835 2005-04-06 Douglas Bates <bates@wisc.edu>
1842 : bates 692
1843 :     * R/AllClass.R : add logical sparse matrix classes
1844 :    
1845 : maechler 687 2005-04-01 Martin Maechler <maechler@stat.math.ethz.ch>
1846 :    
1847 :     * R/dgTMatrix.R: add "[" method for triplet matrices
1848 :     * R/sparseMatrix.R: and other sparse ones; --> add show() for sparse
1849 :    
1850 : bates 835 2005-03-31 Douglas Bates <bates@wisc.edu>
1851 : maechler 687
1852 :     * DESCRIPTION (Version): release 0.95-5 to CRAN
1853 :    
1854 :     * R/dMatrix.R: add %*%, crossprod and solve "fallback" methods
1855 :     * R/sparseMatrix.R: %*%, crossprod()
1856 :     * R/dgeMatrix.R: more "fallback" methods for numeric/dense matrices
1857 :     * man/*.Rd: move method definitions to 'Matrix' and 'dMatrix'
1858 :     * src/lmer.c (lmer_fitted): fix thinko
1859 :    
1860 : maechler 676 2005-03-26 Martin Maechler <maechler@stat.math.ethz.ch>
1861 :    
1862 :     * R/AllClass.R: add two virtual sparse classes ``on top''
1863 :    
1864 :     2005-03-24 Martin Maechler <maechler@stat.math.ethz.ch>
1865 :    
1866 :     * R/AllClass.R (setClass): use "VIRTUAL" for the virtual classes;
1867 :     correspondingly fix examples and tests/ since new()
1868 :     doesn't work for virtual classes.
1869 :    
1870 : maechler 658 2005-03-17 Martin Maechler <maechler@stat.math.ethz.ch>
1871 :    
1872 :     * R/Matrix.R (as.matrix): method and one for unname()
1873 :     * tests/dpoMatrix.R: tests should now be less platform dependent;
1874 :     also run for R 2.1.0; using as.matrix()
1875 :    
1876 : bates 835 2005-03-15 Douglas Bates <bates@wisc.edu>
1877 : maechler 658
1878 :     * R/pMatrix.R: "pMatrix" class added
1879 :     * ....
1880 :    
1881 : bates 835 2005-03-14 Douglas Bates <bates@wisc.edu>
1882 : bates 645
1883 :     * R/dtpMatrix.R: Add unpack method and an example.
1884 :    
1885 :     * src/dsyMatrix.c (dsyMatrix_trf): Add BunchKaufman factorization
1886 :     of general symmetric matrices and associated S4 methods.
1887 :    
1888 : maechler 658 2005-03-10 Martin Maechler <maechler@stat.math.ethz.ch>
1889 :     +
1890 :     2005-03-05 Martin Maechler <maechler@stat.math.ethz.ch>
1891 :    
1892 :     * R/dgeMatrix.R (setAs): and many other files: more coercion,
1893 :     crossprod() and "%*%" methods added; tests, too.
1894 :     * tests/matprod.R: new, for testing these
1895 :    
1896 : bates 835 2005-03-03 Douglas Bates <bates@wisc.edu>
1897 : bates 599
1898 :     * src/lmer.c (lmer_fitted): Added.
1899 :    
1900 : bates 835 2005-03-02 Douglas Bates <bates@wisc.edu>
1901 : bates 596
1902 :     * R/dsTMatrix.R: Conversion from dsTMatrix to dsCMatrix
1903 :    
1904 : bates 835 2005-02-28 Douglas Bates <bates@wisc.edu>
1905 : bates 582
1906 :     * src/*.c,po/,inst/po: Internationalization and localization of
1907 :     the package.
1908 :    
1909 :     * src/ldl.[ch]: Removed these as their contents are referenced in the
1910 :     R_ldl.c file.
1911 :    
1912 :     * src/flame.[ch]: Removed these source files.
1913 : maechler 658
1914 : bates 582 * src/dtrMatrix.c (make_array_triangular): Move to Mutils
1915 :    
1916 :     * src/LU.[ch],src/init.c: absorb in factorizations
1917 :    
1918 :     * src/Mutils.h: prepare for internationalization
1919 :    
1920 :     * src/cblas.h: move the enum definitions to Mutils.h and remove
1921 :     this file
1922 :    
1923 : maechler 578 2005-02-26 Martin Maechler <maechler@stat.math.ethz.ch>
1924 :    
1925 : maechler 579 * R/dgeMatrix.R: provide "dimnames" and "dimnames<-" methods
1926 :    
1927 :     * R/dtrMatrix.R: fix t() method
1928 :    
1929 : maechler 578 * R/dgeMatrix.R: define group methods "Arith", "Math", "Math2"
1930 : maechler 658 * NAMESPACE: export them (and import generics from "methods")
1931 : maechler 578 * tests/group-methods.R : and test them.
1932 :    
1933 :     * src/dtrMatrix.c (dtrMatrix_as_dgeMatrix): prevent seg.fault in
1934 :     border case
1935 :    
1936 :     2005-02-24 Douglas Bates <bates@stat.wisc.edu>
1937 :    
1938 : maechler 658 * DESCRIPTION (Version): 0.95-2 released to CRAN
1939 : maechler 578
1940 :     * src/dgBCMatrix.c:
1941 :     * src/lmer.c: many changes
1942 :     * ...
1943 :    
1944 : maechler 512 2005-02-04 Martin Maechler <maechler@stat.math.ethz.ch>
1945 :    
1946 :     * R/Matrix.R: add more sophisticated show() method.
1947 :    
1948 : maechler 578 2005-02-02 Douglas Bates <bates@stat.wisc.edu>
1949 :    
1950 :     * */* : almost complete reorganization of classes.
1951 :    
1952 : bates 835 2005-01-26 Douglas Bates <bates@wisc.edu>
1953 : bates 460
1954 :     * R/AllGeneric.R: Added matrix exponential generic expm and a method
1955 :     for the geMatrix class.
1956 :    
1957 : bates 835 2005-01-24 Douglas Bates <bates@wisc.edu>
1958 : bates 460
1959 :     * src/Makefile (clean): Remove *.a and *.so
1960 :    
1961 :     * man/cscBlocked-class.Rd: Remove reference to the lmer-class.
1962 :    
1963 : bates 835 2005-01-23 Douglas Bates <bates@wisc.edu>
1964 : bates 460
1965 : maechler 658 * src/lmer.c (Lind): Definition of Lind was backwards. This only
1966 : bates 460 had an effect in cases with more than 2 grouping factors.
1967 :    
1968 : bates 835 2005-01-03 Douglas Bates <bates@wisc.edu>
1969 : bates 415
1970 :     * src/lmeRep.c (lmer_variances): change from lmeRep to lmer
1971 :    
1972 : bates 835 2004-12-23 Douglas Bates <bates@wisc.edu>
1973 : bates 410
1974 :     * src/init.c (R_init_Matrix): Reorder calls to R_registerRoutines
1975 :     and R_useDynamicSymbols (suggested by B.D.Ripley).
1976 :    
1977 : bates 835 2004-12-14 Douglas Bates <bates@wisc.edu>
1978 : bates 392
1979 :     * R/sscMatrix.R: Add determinant methods
1980 :    
1981 :     * src/triplet.[ch],src/init.c (triplet_to_matrix): Add a coercion
1982 :     for tripletMatrix to matrix.
1983 :    
1984 : bates 835 2004-12-13 Douglas Bates <bates@wisc.edu>
1985 : bates 388
1986 : bates 392 * R/AllClass.R (.onLoad): Eliminate the bbCrosstab class, which is
1987 :     no longer used.
1988 :    
1989 : bates 388 * src/R_ldl.c: Created an R-specific version of the ldl.[ch] files
1990 :     with dynamic allocation of scratch arrays.
1991 :    
1992 :     * src/ssclme.c (ssclme_copy_ctab): Fixed bug in creation of ZtZ
1993 :     for multivariate random effects with multiple grouping factors.
1994 :     Fixes part but not all of #15.
1995 :    
1996 : bates 835 2004-12-03 Douglas Bates <bates@wisc.edu>
1997 : bates 375
1998 :     * src/lmeRep.c (lmeRep_factor): order of operations for multiple
1999 :     scalar grouping factors corrected.
2000 :    
2001 : bates 835 2004-11-29 Douglas Bates <bates@wisc.edu>
2002 : bates 375
2003 :     * src/bCrosstab.c: remove diag_update which is no longer used
2004 :    
2005 : bates 835 2004-11-16 Douglas Bates <bates@wisc.edu>
2006 : bates 350
2007 :     * src/Metis_utils.c: Move metis.h include to C sources so that the
2008 :     .h file can be included.
2009 :    
2010 : bates 835 2004-11-12 Douglas Bates <bates@wisc.edu>
2011 : bates 342
2012 : bates 350 * src/LU.c,geMatrix.c,trMatrix.c, etc.:
2013 : bates 342 Complete allocation of slots in NEW_OBJECT.
2014 :    
2015 :     * src/Mutils.h: Moved list of symbols to an include file
2016 :    
2017 : bates 835 2004-11-11 Douglas Bates <bates@wisc.edu>
2018 : bates 342
2019 :     * src/geMutils.c (Matrix_init): remove unused function
2020 :    
2021 : bates 835 2004-11-10 Douglas Bates <bates@wisc.edu>
2022 : bates 342
2023 :     * src/cscMatrix.c (csc_to_imagemat): removed unused function
2024 :    
2025 : bates 835 2004-11-05 Douglas Bates <bates@wisc.edu>
2026 : bates 327
2027 :     * src/Makefile.win (SOURCES_C): Keep consistent with Makefile
2028 :    
2029 : bates 835 2004-10-27 Douglas Bates <bates@wisc.edu>
2030 : bates 303
2031 :     * R/pdmatrix.R: remove PACKAGE="Matrix" in .Call calls
2032 :    
2033 : bates 835 2004-10-04 Douglas Bates <bates@wisc.edu>
2034 : bates 296
2035 :     * src/init.c: Created R_init_Matrix and added registration of C
2036 :     routines.
2037 :    
2038 : bates 835 2004-10-02 Douglas Bates <bates@wisc.edu>
2039 : bates 283
2040 :     * R/tripletMatrix.R: Force a require(lattice) for the image methods.
2041 :    
2042 : bates 835 2004-06-15 Douglas Bates <bates@wisc.edu>
2043 : bates 229
2044 :     * man/trMatrix-class.Rd: Escape the % chars in .Rd files.
2045 :    
2046 : bates 111 2004-04-20 Douglas Bates <bates@stat.wisc.edu>
2047 :    
2048 :     * src/Makefile.win ($(SHLIB)): Modifications per Uwe Ligges.
2049 :    
2050 : bates 109 2004-04-19 Douglas Bates <bates@stat.wisc.edu>
2051 :    
2052 :     * src/ssclme.c (ssclme_update_mm): fix logic error in
2053 :     ssclme_update_mm
2054 :    
2055 : bates 105 2004-04-18 Douglas Bates <bates@stat.wisc.edu>
2056 :    
2057 :     * src/ssclme.c (ssclme_coef, ssclme_coefGets): Create consistency
2058 :     in the order of unconstrained and constrained parameters.
2059 :     (ssclme_gradient): Added the gradients (not yet correct for
2060 :     multidimensional, unconstrained case).
2061 :    
2062 : bates 78 2004-04-14 Douglas Bates <bates@stat.wisc.edu>
2063 :    
2064 :     * src/ssclme.c (ssclme_EMsteps): Fix logic in REML update
2065 :    
2066 :     * src/Makefile.win: Remove unneeded ranlib call
2067 :    
2068 : bates 71 2004-04-12 Douglas Bates <bates@stat.wisc.edu>
2069 :    
2070 :     * DESCRIPTION (Version): New release
2071 :    
2072 :     * src/Makefile.win: Update Makefile.win to umfpack removal.
2073 :    
2074 : bates 49 2004-04-05 Douglas Bates <bates@bates2_home>
2075 :    
2076 :     * src/triplet_to_col.c: Create triplet_to_col as a native
2077 : maechler 658 function, not the version from umfpack. There were problems with
2078 : bates 49 the configuration of UMFPACK for 64-bit processors and there was
2079 :     only one umfpack routine being used so I moved it here.
2080 :    
2081 : bates 45 2004-04-04 Douglas Bates <bates@bates2_home>
2082 :    
2083 :     * src/ssclme.c (ssclme_variances): New function.
2084 :    
2085 : bates 28 2004-03-28 Douglas Bates <bates@bates2_home>
2086 :    
2087 :     * src/ssclme.c (ssclme_fitted): Added function.
2088 :    
2089 : bates 22 2004-03-27 Douglas Bates <bates@bates2_home>
2090 :    
2091 :     * src/ssclme.c (ssclme_transfer_dimnames): Add new function to
2092 :     store the dimnames in the XtX and bVar slots
2093 :     (ssclme_update_mm): Change the dimensions of the bVar slot
2094 :     components and the returned value from ssclme_ranef.
2095 :    
2096 : bates 10 2004-03-18 Douglas Bates <bates@stat.wisc.edu>
2097 :    
2098 :     * R/{pdMat.R,pdIdent.R,pdLogChol.R,pdMatrixLog.R,pdNatural.R},
2099 :     src/{pdMat.c,pdIdent.c,pdLogChol.c,pdNatural.c},
2100 :     tests/{pdCompSymm.R,pdDiag.R,pdIdent.R,pdLogChol.R,pdNatural.R},
2101 :     man/{pdMat-class.Rd,pdmatrix-class.Rd,corrmatrix-class.Rd,
2102 :     pdDiag-class.Rd,pdIdent-class.Rd,pdNatural-class.Rd,
2103 :     pdLogChol-class.Rd,coefGets.Rd,pdCompSymm-class.Rd,
2104 :     pdfactor-class.Rd,pdFactor.Rd,pdMatrix.Rd,
2105 :     pdBlocked-class.Rd},AllClass.R,AllGeneric.R:
2106 :     Moved the pdMat classes from the lme4 package.
2107 :    
2108 :     2004-03-02 Douglas Bates <bates@stat.wisc.edu>
2109 :    
2110 :     * man/ssclme-class.Rd: Update definition and documentation of the
2111 :     ssclme class to include the DIsqrt slot.
2112 :    
2113 :     * src/ssclme.c (ssclme_deviance): Modify order of computation
2114 :     (much faster using dsyrk, a level 3 BLAS routine).
2115 :    
2116 :     * src/Makefile (SUBLIBS): Change definition (K. Hornik)
2117 :    
2118 :     2004-02-28 Douglas Bates <bates@stat.wisc.edu>
2119 :    
2120 :     * tests/ssclme.R: Modify the test to account for the permutation
2121 :     of the levels of the grouping factors.
2122 :    
2123 :     2004-02-23 Douglas Bates <bates@stat.wisc.edu>
2124 :    
2125 :     * R/ssclme.R,src/ssclme.c (ssclme): Move slots of sscCrosstab slot
2126 :     directly into the ssclme class definition.
2127 :    
2128 :     2004-02-22 Douglas Bates <bates@stat.wisc.edu>
2129 :    
2130 :     * DESCRIPTION (Date): New release
2131 :    
2132 :     * man/ssclme-class.Rd: new file.
2133 :    
2134 :     * src/ssclme.c (ssclme_loglik): major revisions in design. It
2135 :     works and it's fast!
2136 :    
2137 :     2004-02-17 Douglas Bates <bates@stat.wisc.edu>
2138 :    
2139 :     * src/taucs/Makefile.win (lib): Change "ar" to "$(AR)" (B.Ripley)
2140 :    
2141 :     2004-02-16 Douglas Bates <bates@stat.wisc.edu>
2142 :    
2143 :     * DESCRIPTION (Date): New release
2144 :    
2145 :     * NAMESPACE: Don't export ssclme.
2146 :    
2147 :     * data/ScotsSec.rda, man/ScotsSec.Rd: Add Scottish secondary
2148 :     school data.
2149 :    
2150 :     2004-02-11 Douglas Bates <bates@stat.wisc.edu>
2151 :    
2152 :     * src/sscCrosstab.c (sscCrosstab): Added a row to the incidence to
2153 :     keep track of the fixed-effects and the response. Counts also
2154 :     gets an extra element, which is always one.
2155 :    
2156 :     * src/ldl.c: Include these routines from Tim Davis' LDL package.
2157 :    
2158 :     2004-02-10 Douglas Bates <bates@stat.wisc.edu>
2159 :    
2160 :     * src/cscMatrix.c (csc_transpose): new function
2161 :    
2162 :     * src/Mutils.c (csc_sort_columns): perm/iperm confusion corrected
2163 :     (csc_components_transpose): new function
2164 :    
2165 :     2004-02-06 Douglas Bates <bates@stat.wisc.edu>
2166 :    
2167 :     * src/triplet.c (triplet_validate): Fix Dim slot on generated
2168 :     triplets
2169 :    
2170 :     2004-01-30 Douglas Bates <bates@stat.wisc.edu>
2171 :    
2172 :     * R/sscCrosstab.R (sscCrosstab): Added sscCrosstab generator function.
2173 :    
2174 :     * src/LU.h (MATRIX_LU_H): Add #ifndef #define ... #endif to this
2175 :     and all other .h files in src.
2176 :    
2177 :     * src/Makefile.win: This and other Makefile.win files contributed
2178 :     by Brian Ripley.
2179 :    
2180 :     2004-01-27 Douglas Bates <bates@stat.wisc.edu>
2181 :    
2182 :     * R/syMatrix.R: Added methods for "%*%".
2183 :    
2184 :     * R/Hilbert.R (Hilbert): Changed Hilbert function to return a
2185 :     poMatrix object.
2186 :    
2187 :     2004-01-26 Douglas Bates <bates@stat.wisc.edu>
2188 :    
2189 :     * man/sscChol-class.Rd,man/mm.Rd,man/y.Rd: Added man pages.
2190 :    
2191 :     2004-01-25 Douglas Bates <bates@bates2_home>
2192 :    
2193 :     * inst/doc/Introduction.Rnw,Comparisons.Rnw: Added vignettes.
2194 :    
2195 :     * R/csc.R: Convert all cscMatrix classes to use Dim slot instead
2196 :     of nrow.
2197 :    
2198 :     2003-12-31 Douglas Bates <bates@stat.wisc.edu>
2199 :    
2200 :     * src/taucs/taucs.h: Moved taucs.h, amd.h, and umfpack.h into
2201 :     subdirectories.
2202 :    
2203 :     2003-12-08 Douglas Bates <bates@stat.wisc.edu>
2204 :    
2205 :     * src/taucs.h: Accidently referred to global header files
2206 :     instead of local files.
2207 :    
2208 :     2003-12-04 Douglas Bates <bates@stat.wisc.edu>
2209 :    
2210 :     * R/AllClass.R: Lots of changes. Removed all the lapack++ code
2211 :     and methods and replaced all classes with S4 classes.
2212 :    
2213 :     2003-04-19 Douglas Bates <bates@stat.wisc.edu>
2214 :    
2215 :     * R/det.R,man/det.Rd: Change name of det generic to determinant
2216 :    
2217 :     * src/R_LapackPP.cc: Change method of calculating determinants
2218 :    
2219 :     2003-02-03 Douglas Bates <bates@stat.wisc.edu>
2220 :    
2221 :     * DESCRIPTION (Version): removed empty data directory as requested
2222 :     by CRAN maintainers. Changed version number and date.
2223 :    
2224 :     2002-10-23 Douglas Bates <bates@stat.wisc.edu>
2225 :    
2226 :     * src/laindex.h: Applied patches from Brian Ripley for compilation
2227 :     under Windows.
2228 :    
2229 :     * Added configure.win and src/Makevars.win as requested by Brian
2230 :     Ripley.
2231 :    
2232 :     2002-05-03 Douglas Bates <bates@stat.wisc.edu>
2233 :    
2234 :     * src/lamatrix.h: Removing pre-1.2.0 compatibility code per Kurt
2235 :     Hornik.
2236 :    
2237 :     2002-04-24 Douglas Bates <bates@stat.wisc.edu>
2238 :    
2239 :     * configure.ac: Replaced configure.in with configure.ac
2240 :     contributed by Kurt Hornik.
2241 :    
2242 :     * aclocal.m4 (ac_clean_files): Replaced this with Kurt Hornik's
2243 :     version for R-1.5.0
2244 :    
2245 : maechler 512
2246 : bates 10 2001-12-10 Douglas Bates <bates@stat.wisc.edu>
2247 :    
2248 :     * man/eigen.Rd: Removed the .Alias in the example

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