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Revision 1787 - (view) (download)

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

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