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Annotation of /pkg/ChangeLog

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Revision 1661 - (view) (download)

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

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