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Annotation of /pkg/ChangeLog

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

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