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Annotation of /pkg/ChangeLog

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

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