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Annotation of /pkg/ChangeLog

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

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