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

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