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Revision 1665 - (view) (download)

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

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