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Revision 1592 - (view) (download)

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

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