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Annotation of /pkg/ChangeLog

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

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