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Annotation of /pkg/ChangeLog

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Revision 1691 - (view) (download)

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

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