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Annotation of /pkg/ChangeLog

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

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