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Annotation of /pkg/ChangeLog

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

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