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Annotation of /pkg/ChangeLog

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Revision 1599 - (view) (download)

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

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