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

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