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Annotation of /pkg/ChangeLog

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

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