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Annotation of /pkg/ChangeLog

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

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