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

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