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Annotation of /pkg/ChangeLog

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

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