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Annotation of /pkg/ChangeLog

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1 : maechler 1635 2006-10-17 Martin Maechler <maechler@stat.math.ethz.ch>
2 :    
3 :     * R/diagMatrix.R (%*%): rep(*, each = .) in Matrix %*% diagonal.
4 :     * tests/matprod.R: add tests for the bug fixed.
5 :    
6 : bates 1624 2006-10-11 Douglas Bates <bates@stat.wisc.edu>
7 :    
8 :     * src/HBMM.[ch]: remove HarwellBoeing format for writing.
9 :     * src/SOURCES_C.mkf (SOURCES_C): no longer compile iohb.c
10 :    
11 :     2006-10-06 Douglas Bates <bates@stat.wisc.edu>
12 :    
13 : bates 1629 * R/d[gs]CMatrix.R: deprecate the writeHB function. Use writeMM instead.
14 : bates 1624
15 : maechler 1618 2006-10-06 Martin Maechler <maechler@stat.math.ethz.ch>
16 :    
17 :     * DESCRIPTION (Version): 0.9975-3
18 :    
19 :     * R/diagMatrix.R (bdiag): new function constructing block diagonal
20 :     (sparse) matrices.
21 :     * man/bdiag.Rd: docu + examples
22 :    
23 : maechler 1619 * R/Csparse.R (replCmat): calling new Csparse_drop() now.
24 :    
25 : maechler 1618 * src/Csparse.c (Csparse_general_to_symmetric, Csparse_drop): new functions
26 :     * R/lsCMatrix.R: three more coercions to lsC (thanks to the above)
27 :    
28 :     * R/diagMatrix.R (Diagonal): '[<-' method for diag.matrices such
29 :     that result is sparse or diagonal (and not dense).
30 :    
31 :     * man/Subassign-methods.Rd: fix examples
32 :    
33 :     * R/Matrix.R (Matrix): Matrix(0, *) or Matrix(*, sparse=TRUE)
34 :     should always return a sparse (and not sometimes a diagonal) matrix.
35 :    
36 : maechler 1615 2006-10-05 Martin Maechler <maechler@stat.math.ethz.ch>
37 :    
38 :     * R/Matrix.R ([<-): also for value "Matrix" or "matrix"
39 :    
40 : bates 1613 2006-10-04 Douglas Bates <bates@stat.wisc.edu>
41 :    
42 :     * DESCRIPTION (Version): 0.9975-2
43 : maechler 1615
44 : bates 1613 * inst/include/Matrix_stubs.c (M_cholmod_sparse_to_triplet): export more symbols
45 :    
46 : bates 1611 2006-10-02 Douglas Bates <bates@R-project.org>
47 :    
48 :     * tests/dg_Matrix.R: Simplify test taking into account new code.
49 :    
50 : maechler 1599 2006-09-29 Martin Maechler <maechler@stat.math.ethz.ch>
51 :    
52 : maechler 1600 * R/Csparse.R (replCmat): improve for missing i / j in non-simple cases
53 :    
54 : maechler 1599 * R/lsTMatrix.R: new files w/ missing methods
55 :     * R/nsTMatrix.R: " 'for completeness'
56 :    
57 :     * tests/Class+Meth.R: a bit less 'not.ok.classes'
58 :    
59 :     * R/Tsparse.R (t): generalized "t" method from "dgT*" to "Tsparse*"
60 :    
61 :    
62 : bates 1595 2006-09-28 Douglas Bates <bates@R-project.org>
63 :    
64 :     * src/dppMatrix.h: Ensure definition of dspMatrix_validate is
65 :     included.
66 :    
67 :     * src/init.c, inst/include/{Matrix.h,Matrix_stubs.h,cholmod.h}:
68 :     Export C-callable functions used in Zt_create in lme4.
69 :    
70 : maechler 1592 2006-09-28 Martin Maechler <maechler@stat.math.ethz.ch>
71 :    
72 :     * DESCRIPTION (Version): 0.9975-1
73 :    
74 :     * tests/simple.R: less checks fail; using NA, found that our
75 :     kronecker() is not base-compatible with NA's.
76 :    
77 :     * R/dMatrix.R: "Compare" method now implemented for all cases
78 :    
79 :     * R/Auxiliaries.R (indTri): == which([lower/upper].tri( * )) new utility
80 :    
81 :     * man/dtpMatrix-class.Rd: mention length of 'x' slot
82 :    
83 :     * src/dtpMatrix.c (dtpMatrix_validate): fix check
84 :     * src/dspMatrix.c (dspMatrix_validate): ditto
85 :    
86 :     * R/dtTMatrix.R (gt2tT): fix ("l" -> "n")
87 :     including coercion to [nl]tTMatrix.
88 :    
89 :     * R/diagMatrix.R (show): print a header line as for other classes.
90 :    
91 :     2006-09-27 Martin Maechler <maechler@stat.math.ethz.ch>
92 :    
93 :     * src/Makefile.win (SUBDIRS): fix typo
94 :    
95 : maechler 1583 2006-09-19 Martin Maechler <maechler@stat.math.ethz.ch>
96 :    
97 :     * DESCRIPTION (Date): ready to release 0.9975-0 to CRAN
98 :    
99 : bates 1577 2006-09-18 Douglas Bates <bates@stat.wisc.edu>
100 :    
101 :     * R/[CT]sparse.R (crossprod and tcrossprod): Handle the cases for x
102 :     symmetric and y missing in R code using %*% (cholmod_aat doesn't
103 :     accept a symmetric matrix).
104 :     * tests/group-methods.R: Uncomment test of crossprod applied to
105 :     lsCMatrix objects.
106 :    
107 : maechler 1575 2006-09-18 Martin Maechler <maechler@stat.math.ethz.ch>
108 :    
109 :     * R/AllClass.R (symmetricMatrix): add validity method (available
110 :     in C for a long time). Many "n..Matrix": drop (wrong) validity arg.
111 :    
112 :     * src/lgCMatrix.c (lgCMatrix_validate): check 'x' slot (!)
113 :    
114 :     * tests/indexing.Rout.save:
115 :     * tests/indexing.R: additions, mainly for 'lsparse'
116 :    
117 :     * R/diagMatrix.R (Diagonal) & coercion to lgTMatrix: fixes for NA
118 :     case.
119 :    
120 :     * R/Auxiliaries.R (nz.NA): new utility now used in nnzero()
121 :    
122 : maechler 1571 2006-09-16 Martin Maechler <maechler@stat.math.ethz.ch>
123 :    
124 : maechler 1572 * R/sparseMatrix.R (prSpMatrix): print logical NAs "visibly"
125 :     as 'N' (1-letter - Ok?)
126 :    
127 : maechler 1571 * tests/group-methods.R: add test for logical + NAs
128 :    
129 :     * R/dMatrix.R ("Compare"): fix to work with NA's
130 :    
131 :     * R/AllClass.R: "Cholesky" etc now inherit from MatrixFactorization.
132 :    
133 :     * src/lgCMatrix.c (ncsc_to_matrix): renamed from lcsc_to_matrix()
134 :     which is implemented.
135 :    
136 : maechler 1565 2006-09-15 Martin Maechler <maechler@stat.math.ethz.ch>
137 :    
138 : maechler 1571 * src/chm_common.c: coerce logical <-> double instead of
139 :     typecasting; needed for "l" matrix handling in cholmod.
140 : maechler 1565
141 : maechler 1571 * tests/other-pkgs.R (graph): small extension in "graph" checks.
142 :    
143 : maechler 1565 * R/sparseMatrix.R (graphNEL -> Tsparse): method for weight case.
144 :     (Tsp2grNEL): other fixes needed
145 :    
146 : maechler 1548 2006-09-11 Martin Maechler <maechler@stat.math.ethz.ch>
147 :    
148 :     * R/AllClass.R ("nMatrix"): and subclasses for "nonzero pattern"
149 :     Matrices, since "lMatrix", also "lsparseM" can have NA
150 :     * R/ndenseMatrix.R, etc: new source files
151 :     * man/nsparseMatrix-classes.Rd, etc: new help files
152 :     * tests/: adaptions
153 :     * src/chm_common.c (chm_dense_to_SEXP): and others:
154 :     new 'Rkind' argument: "l*" and "d*" both use CHOLMOD_REAL
155 : maechler 1582 * src/Csparse.c, etc: ditto
156 : maechler 1548
157 : bates 1546 2006-09-11 Douglas Bates <bates@R-project.org>
158 :    
159 :     * src/Mutils.[ch],init.c inst/include/*.h: Move the
160 :     alloc_d**Matrix functions to the lme4 package.
161 :    
162 : bates 1543 2006-09-09 Douglas Bates <bates@R-project.org>
163 :    
164 :     * src/dsCMatrix.c (dsCMatrix_Cholesky): igoring LDL = FALSE now
165 : maechler 1544 fixed
166 : bates 1543
167 : maechler 1544 2006-09-09 Martin Maechler <maechler@stat.math.ethz.ch>
168 :    
169 : maechler 1548 * R/lMatrix.R: new
170 :    
171 : maechler 1544 * R/sparseMatrix.R (Tsp2grNEL): do not yet use graph::foo()
172 :    
173 :     * R/dgeMatrix.R: do not define tcrossprod() methods for "matrix"
174 : maechler 1582 * man/tcrossprod.Rd: ditto
175 : maechler 1544
176 : bates 1538 2006-09-08 Douglas Bates <bates@stat.wisc.edu>
177 :    
178 :     * inst/include/Matrix_stubs.c,Matrix.h: Add declarations and stubs
179 :     for exported functions
180 :     * src/Makefile, src/CHOLMOD/Lib/Makefile, src/Metis,CAMD,CCOLAMD:
181 :     Remove partitioning algorithms for sparse matrix reordering. The
182 :     copyright on the Metis code was problematic and the methods were
183 :     rarely used.
184 :     * src/triplet_to_col.[ch],MMHB.[ch]: Remove triplet_to_col. Such
185 :     operations are now done entirely in CHOLMOD code.
186 :    
187 : bates 1517 2006-09-06 Douglas Bates <bates@R-project.org>
188 :    
189 :     * src/Mutils.h: Remove functions that are no longer used.
190 :    
191 : bates 1507 2006-09-04 Douglas Bates <bates@R-project.org>
192 :    
193 :     * src/dtCMatrix.c (dtCMatrix_validate): rename functions.
194 :     * src/DEPS.mkf: update
195 :    
196 : maechler 1481 2006-09-02 Martin Maechler <maechler@stat.math.ethz.ch>
197 :    
198 :     * created branches/Matrix-for-R-2.3.x; on trunk: do
199 :     * DESCRIPTION (Version): 0.9975-0
200 :     (Depends): R (>= 2.4.0)
201 :    
202 : bates 1475 2006-09-01 Douglas Bates <bates@R-project.org>
203 :    
204 :     * R/sparseMatrix.R: Added direct method to CsparseMatrix from graphNEL
205 :    
206 : maechler 1472 2006-09-01 Martin Maechler <maechler@stat.math.ethz.ch>
207 :    
208 :     * R/sparseMatrix.R: add coercion from "ANY" to "sparseMatrix"
209 :     * R/denseMatrix.R: add coercion from "ANY" to "denseMatrix"
210 :    
211 :     * R/Matrix.R ([): use nargs() to disambiguate M[i] and M[i,]
212 :    
213 :     2006-08-31 Martin Maechler <maechler@stat.math.ethz.ch>
214 :    
215 :     * R/sparseMatrix.R (Arith): moved Arith group method one-level up
216 :     from "dsparse" to "sparse" and now go via "Csparse" instead of "dgC"
217 : maechler 1582 * R/dsparseMatrix.R: ditto
218 :     * R/Csparse.R: ditto
219 : maechler 1472
220 :     2006-08-31 Martin Maechler <maechler@stat.math.ethz.ch>
221 :    
222 :     * R/dMatrix.R (Compare): improve availability of "<", etc
223 :     * R/Auxiliaries.R (asTuniq): new; also make use of R 2.4.x print(*,max)
224 :    
225 : maechler 1467 2006-08-30 Martin Maechler <maechler@stat.math.ethz.ch>
226 :    
227 :     * R/dgCMatrix.R: aargh: "Arith(<dgC>, numeric)" was wrong because
228 :     of a 0-index which was used as 1-index (..hmm)
229 :    
230 :     * R/sparseMatrix.R (prSpMatrix): fix printing an all-0 sparse Matrix
231 :    
232 :     * R/Auxiliaries.R (all0, is0): for 0-testing in presence of NA's
233 :     * R/Auxiliaries.R (isTriMat): use all0() for 0-testing.
234 : maechler 1582 (.is.diagonal): ditto
235 : maechler 1467
236 :     * R/lgTMatrix.R: as("matrix", "lgTMatrix"): warn about NA's
237 :    
238 :     * R/Matrix.R (Matrix): also work for NA data
239 :    
240 : maechler 1455 2006-08-28 Martin Maechler <maechler@stat.math.ethz.ch>
241 :    
242 :     * R/Matrix.R (Matrix): + 'forceCheck' argument; dimnames setting
243 :     in all cases.
244 :    
245 : bates 1453 2006-08-27 Douglas Bates <bates@R-project.org>
246 :    
247 :     * src/dense.[ch],init.c, R/ddenseMatrix.R, man/band.Rd
248 :     (ddense_band): Added triu, tril and band for ddenseMatrix objects.
249 :    
250 : maechler 1447 2006-08-25 Martin Maechler <maechler@stat.math.ethz.ch>
251 :    
252 :     * src/Mutils.c (dup_mMatrix_as_dgeMatrix): added all subclasses of
253 :     subclasses of "ddenseMatrix"
254 :     * src/init.c et al: outcomment dtrM*_as_dge* and dsyM*_as_dge*_
255 :     * R/ddenseMatrix.R et al: setAs("ddenseMatrix", "dgeMatrix", ..)
256 :     instead of half dozen specialized ones.
257 :    
258 : bates 1445 2006-08-25 Douglas Bates <bates@R-project.org>
259 :    
260 :     * R/lmer.R (qqmath method): Bug fix provided by Emmanuel Tillard
261 :     <tillard@cirad.fr> - ordering standard errors to match effects.
262 :    
263 : bates 1439 2006-08-24 Douglas Bates <bates@R-project.org>
264 : bates 1431
265 : bates 1439 * src/lsCMatrix.c (lsCMatrix_trans): Remove lsCMatrix_chol based
266 :     on R_ldl.
267 :     * R/lCholCMatrix.R,
268 :     src/[dl]CholCMatrix.[ch],R_ldl.[ch],Metis_utils.[ch]: removed
269 :     * src/dsCMatrix.c (dsCMatrix_to_dgTMatrix): use CHOLMOD
270 :     * many files in ./R and ./src: Use more general version of
271 :     dup_mMatrix_as_dgeMatrix to simplify method definitions.
272 : bates 1442 * src/Mutils.c (dup_mMatrix_as_dgeMatrix): Add ddiMatrix,
273 :     dtpMatrix, dspMatrix and dppMatrix conversions.
274 :    
275 : maechler 1447
276 : bates 1439 2006-08-23 Douglas Bates <bates@R-project.org>
277 :    
278 :     * R/AllClass.R,lCholCMatrix.R,src/SOURCES_C.mkf,init.c,NAMESPACE:
279 :     Remove classes lCholCMatrix and dCholCMatrix based on R_ldl code.
280 : bates 1431 * src/dgeMatrix.c: Ensure 'factors' slot exists in result of
281 :     dgeMatrix_crossprod (may need to do this in other places).
282 :     * R/AllGeneric.R,dsCMatrix.R, src/dscMatrix.[ch]: Add Cholesky
283 :     generic and method for dsCMatrix. Use CHOLMOD for chol().
284 :    
285 : bates 1414 2006-08-22 Douglas Bates <bates@R-project.org>
286 :    
287 :     * src/Mutils.c (dup_mMatrix_as_dgeMatrix): updated for general
288 :     types of classed Matrices, matrices or numeric or logical vectors.
289 : bates 1423 * src/init.c: register dup_mMatrix_as_dgeMatrix for coercions.
290 :     * src/chm_common.c,Mutils.h (as_cholmod_factor): Move check_class
291 :     to Mutils.h (as an inline) and change name to Matrix_check_class;
292 :     fixes in as_cholmod_factor and chm_factor_to_SEXP.
293 :     * src/dsCMatrix.[ch]: Use CHOLMOD for dsCMatrix_chol and
294 :     dsCMatrix_matrix_solve. Comment out vestigial functions.
295 :     * src/Csparse.c: use diag_P and uplo_P macros.
296 : maechler 1447
297 : bates 1405 2006-08-21 Douglas Bates <bates@R-project.org>
298 :    
299 :     * src/lmer.c (internal_mer_RZXinv): Fix memory leak caught by
300 : maechler 1447 valgrind.
301 : bates 1411 * tests/matprod.R: Add tests to verify that 'solve' and '%*%' are
302 :     inverses.
303 :     * src/sparseQR.c (sparseQR_validate): add new validation test, fix
304 :     -Wall warnings.
305 :     * src/dppMatrix.c,dtrMatrix.c,dgCMatrix.c,dgeMatrix.c,dspMatrix.c:
306 :     Use dup_mMatrix_as_dgeMatrix.
307 : maechler 1447
308 : bates 1403 2006-08-20 Douglas Bates <bates@R-project.org>
309 :    
310 :     * src/sparseQR.c: Fix thinko in sparseQR_resid_fitted.
311 :     * tests/sparseQR.R: Added
312 :     * man/sparseQR-class.Rd: Document methods for qr.* generics
313 :     * R/sparseQR.R: Return correct # of coefs; fix cut-and-paste errors
314 :    
315 : bates 1398 2006-08-19 Douglas Bates <bates@R-project.org>
316 :    
317 :     * NAMESPACE, R/sparseQR.R, src/init.c,sparseQR.[ch],SOURCES_C.mkf:
318 :     Added methods for sparseQR for qr.qy, qr.qty, qr.coef, qr.resid
319 :     and qr.fitted.
320 :     * src/Mutils.[ch]: Added dup_mMatrix_as_dgeMatrix utility
321 :     * src/dgCMatrix.c: Check for ordering before storing q in dgCMatrix_QR
322 :    
323 : maechler 1389 2006-08-18 Martin Maechler <maechler@stat.math.ethz.ch>
324 :    
325 :     * R/AllGeneric.R: add "qr" and "chol" generics; via 'trick' since
326 :     the base version has no "..." argument.
327 :    
328 :     * R/sparseMatrix.R (prSpMatrix): fix the triangular unit diagonal case.
329 :    
330 :     * R/Matrix.R: define and
331 :     * NAMESPACE: export as.numeric() and as.logical() methods.
332 :     Let's hope these do not badly slow down something...
333 :     Finally export the zapsmall() method.
334 :    
335 : bates 1388 2006-08-17 Douglas Bates <bates@R-project.org>
336 :    
337 :     * src/dgCMatrix.[ch] (dgCMatrix_matrix_solve), src/init.c,
338 :     R/dgCMatrix.R: solve methods for dgCMatrix and dense RHS.
339 :     * src/dtCMatrix.c :Remove code that is no longer used
340 :     * R/dtCMatrix.R: Use C code for diagU2N in CsparseMatrix classes
341 :    
342 : bates 1370 2006-08-14 Douglas Bates <bates@R-project.org>
343 :    
344 : bates 1373 * src/Csparse.[ch],init.c (Csparse_to_logical): Added utilities
345 :     Csparse_to_logical and Csparse_symmetric_to_general.
346 :     * R/dgCMatrix.R,dsCMatrix.R,Csparse.R : Consolidate general
347 : maechler 1389 coercion methods between CsparseMatrix and TsparseMatrix.
348 : bates 1373
349 :     2006-08-14 Douglas Bates <bates@R-project.org>
350 :    
351 : bates 1370 * R/dtCMatrix.R,dgCMatrix.R,Csparse.R src/init.c,dgCMatrix.[ch],
352 :     Csparse.[ch],chm_common.c,dense.c : Use CHOLMOD code and methods
353 :     for CsparseMatrix, TsparseMatrix, denseMatrix or matrix when
354 :     possible.
355 :    
356 : bates 1368 2006-08-12 Douglas Bates <bates@R-project.org>
357 :    
358 :     * src/chm_common.[ch],Csparse.[ch],Tsparse.[ch],CHMfactor.c,dtTMatrix.c,
359 :     dgTMatrix.c,dgCMatrix.c,dsCMatrix.c,dtTMatrix.c, R/dsTMatrix.R,
360 :     Tsparse.R,Csparse.R,dgTMatrix.R,dsCMatrix.R,lsCMatrix.R:
361 :     generalize conversions between TsparseMatrix, CsparseMatrix,
362 :     denseMatrix and matrix. Preserve triangularity property and
363 :     propagate Dimnames in the easy cases.
364 :    
365 : bates 1365 2006-08-10 Douglas Bates <bates@R-project.org>
366 :    
367 :     * src/lmer.c: adjust checks in glmer_init for S4SXP
368 :     * tests/validObj.R: check of all(eq) should be all(eq@x) - worked
369 :     before S4SXP but for the wrong reasons.
370 :    
371 : bates 1354 2006-08-08 Douglas Bates <bates@R-project.org>
372 :    
373 : bates 1360 * src/Csparse.c (Csparse_crossprod): tcrossprod result has stype = -1.
374 :     Later modified to return the upper triangle only.
375 :     * R/dgTMatrix.R: Remove vestigial crossprod and tcrossprod methods.
376 : maechler 1389
377 : bates 1352 2006-08-07 Douglas Bates <bates@R-project.org>
378 :    
379 :     * src/Csparse.c (Csparse_crossprod): Set stype on result to avoid
380 :     R-level conversion to a sparse symmetric class.
381 :     * R/Tsparse.R,R/Csparse.R (crossprod and tcrossprod methods):
382 :     Remove conversion to sparse symmetric classes (now done in C code).
383 :    
384 : maechler 1349 2006-08-07 Martin Maechler <maechler@stat.math.ethz.ch>
385 :    
386 : maechler 1351 * R/dgCMatrix.R: disable old crossprod and tcrossprod methods
387 :     * man/band.Rd: adapt the \dontshow{} unit test.
388 :    
389 :     2006-08-07 Martin Maechler <maechler@stat.math.ethz.ch>
390 :    
391 : maechler 1349 * DESCRIPTION (Version): 0.995-14 for CRAN
392 :    
393 :     * tests/other-pkgs.R: oops: library(Matrix) outside *if* !
394 :    
395 :     * R/sparseMatrix.R (Tsp2grNEL): fixed Tsparse -> graph coercion
396 :     * tests/other-pkgs.R: more checks, sparseMatrix -> graph
397 :    
398 :     * R/Auxiliaries.R (as_Tsparse, as_Rsparse): new
399 :     * R/Tsparse.R (tril, triu, band): methods
400 : bates 1352 * R/dgRMatrix.R (tril, ...): ditto
401 :     * man/band.Rd: ditto
402 : maechler 1349
403 :     2006-08-04 Martin Maechler <maechler@stat.math.ethz.ch>
404 :    
405 :     * R/Matrix.R (head, tail): directly use utils:::head.matrix
406 :     to be up-to-date automatically.
407 :    
408 : maechler 1346 2006-08-03 Martin Maechler <maechler@stat.math.ethz.ch>
409 :    
410 :     * DESCRIPTION (Version): 0.995-13 to be released to CRAN
411 :    
412 :     * DESCRIPTION (Lazydata): no, instead of 'yes' because it fails for:
413 :     * data/CAex.R, inst/external/CAex_slots.rda: replacing data/CAex.rda
414 :     * data/KNex.R, inst/external/KNex_slots.rda: replacing data/KNex.rda
415 :     such that the S4 objects are always created by the current version
416 :     of R and 'Matrix' class definitions.
417 :    
418 : bates 1342 2006-08-01 Douglas Bates <bates@R-project.org>
419 :    
420 :     * R/lmer.R (LMEoptimize method), tests/lmer.R,
421 : maechler 1346 inst/external/test3comp.rda: Added warnings for convergence on
422 : bates 1342 boundary and test cases.
423 :    
424 :     * src/lmer.c (mer_postVar): Modified to return the variances that
425 :     are marginal to the fixed effects, not conditional on them (which
426 :     is what the bVar slot contents represent).
427 :    
428 : bates 1338 2006-07-31 Douglas Bates <bates@R-project.org>
429 :    
430 :     * NAMESPACE, src/lmer.c, R/lmer.R (hatTrace): Add the hatTrace
431 :     function which calls the C function mer_hat_trace2.
432 : maechler 1346
433 : bates 1342 * man/ranef.Rd: Include description of "postVar" argument and
434 :     producing a caterpillar plot.
435 : bates 1338
436 : maechler 1335 2006-07-31 Martin Maechler <maechler@stat.math.ethz.ch>
437 :    
438 :     * NAMESPACE: change "correlation" to "corMatrix"
439 :     * R/AllClass.R: to avoid clash with S3 class in 'nlme'.
440 : bates 1352 * R/dpoMatrix.R: ditto
441 :     * R/lmer.R: ditto
442 : maechler 1335
443 : bates 1338 2006-07-28 Douglas Bates <bates@R-project.org>
444 :    
445 :     * src/lmer.c (internal_mer_RZXinv): Split the calculation of the
446 :     RZXinv slot's contents into a separate internal function that can
447 :     be used in mer_hat_trace.
448 :    
449 : maechler 1331 2006-07-22 Martin Maechler <maechler@stat.math.ethz.ch>
450 :    
451 :     * R/Matrix.R: Coercions "Matrix" -> (sparse|dense)Matrix
452 :     via new smart
453 :     * R/Auxiliaries.R (as_Csparse, as_dense, .M.shapse): new
454 :     utility functions.
455 :    
456 :    
457 : maechler 1330 2006-07-21 Martin Maechler <maechler@stat.math.ethz.ch>
458 :    
459 : maechler 1331 * R/Csparse.R (tril, triu, band): do return *triangular* classed
460 :     matrices when appropriate; band() even symmetric ones.
461 :     (replCmat): extend to potentially all "CsparseMatrix"
462 :     * R/Tsparse.R (replTmat): extend to all "TsparseMatrix"; hence
463 :     allow subassignment for special sparse matrices.
464 :    
465 :     * R/Auxiliaries.R (as_geClass): factor out the .M.kind() functionality
466 :    
467 : maechler 1330 * src/lmer.c (mer_MCMCsamp, glmer_MCMCsamp): new 'verbose'
468 :     argument; in glmer_*(): print only if(verbose).
469 :    
470 :     speed-optimize a few places by moving REAL(.) out of loops.
471 :    
472 :     * src/lmer.h, src/init.h, R/lmer.R: related to above.
473 :    
474 : maechler 1329 2006-07-20 Martin Maechler <maechler@stat.math.ethz.ch>
475 :    
476 :     * R/Matrix.R("["): disable ("Matrix", i = "logical", j = "missing"),
477 :     since that wrongly triggers also for M[ logi , ]
478 :    
479 :     * R/denseMatrix.R: "[" methods now also work e.g. when indexing
480 :     a symmetric matrix that results in a non-symmetric one.
481 :     * R/Auxiliaries.R (as_geClass): new function used in "[" above.
482 :    
483 :     * R/dMatrix.R: make round(M) work as round(M, 0)
484 :    
485 :     * R/dgTMatrix.R (image): coordinate system and axis now use
486 :     1-based indices, not 0-based ones.
487 :    
488 :     * R/Tsparse.R (.ind.prep for "["): get rid of max(<empty>) warning.
489 :     * tests/indexing.R: test it.
490 :    
491 :     * NAMESPACE: export isSymmetric(); has been a generic in "base" for a while;
492 :     * man/isSymmetric-methods.Rd: and document it.
493 :    
494 :     * R/SparseM-conv.R: added coercion methods for some 'SparseM' matrices.
495 :     * man/SparseM-conv.Rd: docu them
496 :    
497 :     * tests/other-pkgs.R: renamed from tests/graph.R and add example
498 :     for 'SparseM' conversions
499 :    
500 :     2006-07-17 Douglas Bates <Douglas.Bates@R-project.org>
501 :    
502 :     * R/Matrix.R (head): added head() and tail() methods.
503 :    
504 :     2006-07-17 Martin Maechler <maechler@stat.math.ethz.ch>
505 :    
506 :     * DESCRIPTION (Version): 0.995-12 released to CRAN
507 :    
508 : maechler 1319 2006-07-15 Martin Maechler <maechler@stat.math.ethz.ch>
509 :    
510 :     * tests/simple.R: add check for correct dsT -> dgT coercion;
511 :     add check for correct printing of symmetric sparse matrices.
512 :    
513 :     * R/Auxiliaries.R (non0ind): return *all* non-0 entry indices also
514 :     for sparse symmetric matrices.
515 :    
516 :     * src/dsTMatrix.c (dsTMatrix_as_dgTMatrix): do not copy the
517 :     diagonal twice.
518 :    
519 : bates 1316 2006-07-11 Douglas Bates <Douglas.Bates@R-project.org>
520 :    
521 :     * src/dsTMatrix.c (dsTMatrix_as_dgTMatrix): Fix a case of INTEGER
522 : maechler 1319 being applied to the x slot (detected by Brian Ripley).
523 : bates 1316
524 : maechler 1315 2006-07-10 Martin Maechler <maechler@stat.math.ethz.ch>
525 :    
526 :     * src/dgCMatrix.c (dgCMatrix_validate): 'p' slot must have correct length.
527 :    
528 :     * R/Auxiliaries.R (isTriC): fix buglet (we were 1-based!)
529 :    
530 :     2006-07-08 Martin Maechler <maechler@stat.math.ethz.ch>
531 :    
532 :     * src/lgCMatrix.c (lgCMatrix_diag): new function
533 :     * R/lgCMatrix.R (diag): for new method
534 :    
535 :     * R/AllClass.R (TsparseMatrix): do use Tsparse_validate
536 :     ==> construction of illegal "*gTMatrix" via new() should
537 :     now be much less easy:
538 :     * tests/Class+Meth.R: assertError() for some illegal "dgT*"
539 :    
540 :     * R/Matrix.R (Matrix): Matrix(0, nrow,ncol) now "goes sparse"
541 :     directly.
542 :     * man/Matrix.Rd: documents it.
543 :    
544 : bates 1311 2006-07-06 Douglas Bates <bates@R-project.org>
545 :    
546 :     * src/pedigree.c (pedigree_inbreeding): Correction in
547 :     initialization. This function is not currently being used and is
548 :     not fully tested.
549 :    
550 : bates 1312 * NAMESPACE, R/{AllClass.R,lmer.R}, src/{init.c,lmer.c}:
551 :     Introduced the glmer class. Added code for mcmcmsamp on glmer
552 :     objects. Modified validity check on pedigree objects to account
553 :     for nonparallel patterns of missingness of parents.
554 : bates 1311
555 : bates 1313 * man/{lmer-class.Rd,mcmcsamp.Rd}: Update documentation for glmer
556 :     class.
557 : maechler 1315
558 :     2006-07-01 Martin Maechler <maechler@stat.math.ethz.ch>
559 :    
560 :     * R/pMatrix.R: coercion pMatrix -> Tsparse
561 :    
562 : bates 1300 2006-06-12 Douglas Bates <bates@R-project.org>
563 :    
564 : maechler 1319 * DESCRIPTION (Version): 0.995-11 released to CRAN
565 :    
566 : bates 1300 * R/lmer.R (mcmcsamp method): Corrected arrangments of names on
567 :     the output from mcmcsamp.
568 :    
569 : bates 1298 2006-06-10 Douglas Bates <bates@R-project.org>
570 :    
571 : bates 1300 * R/lmer.R (simulestimate): added C code for calculating the trace
572 :     of the hat matrix.
573 : bates 1298
574 : maechler 1295 2006-06-09 Martin Maechler <maechler@stat.math.ethz.ch>
575 :    
576 :     * R/diagMatrix.R (setAs): define coercion methods to sparse matrix
577 :     classes.
578 : maechler 1315 * R/sparseMatrix.R etc: multiplication of diagonal and sparse
579 : maechler 1295
580 : maechler 1290 2006-06-08 Martin Maechler <maechler@stat.math.ethz.ch>
581 :    
582 :     * R/dgTMatrix.R (colSums): etc. All four of
583 :     colSums(), rowSums(), colMeans(), rowMeans() now should work for
584 :     all "Matrices".
585 :    
586 : bates 1288 2006-06-01 Douglas Bates <bates@stat.wisc.edu>
587 :    
588 :     * R/lmer.R (panel.ci): Add a reference line at zero and a
589 :     background grid to the qqmath plot of ranef.lmer.
590 :    
591 : bates 1287 2006-05-30 Douglas Bates <bates@stat.wisc.edu>
592 : bates 1284
593 : bates 1287 * R/lmer.R (expandSlash): Functions (non-exported) to allow nested
594 :     grouping factors to be specified in the formula as (1|foo/bar).
595 :    
596 :     2006-05-27 Douglas Bates <bates@stat.wisc.edu>
597 :    
598 : bates 1284 * R/lmer.R (findbars and others): Change check of is.numeric to
599 :     !is.language to resolve the bug reported by Jacob Wegelin.
600 :    
601 :     * src/pedigree.c (pedigree_inbreeding): Initial implementation of
602 :     code to evaluate inbreeding coefficients without calculating T,
603 :     based on code in Sargolzaei and Iwaisaki's paper.
604 :    
605 : bates 1283 2006-05-27 Douglas Bates <bates@stat.wisc.edu>
606 :    
607 :     * R/{lmer.R,AllGeneric.R}, src/{init.c,lmer.[ch]}: Added local
608 :     generic and mer methods for isNested and denomDF. This denomDF was
609 :     an attempt to emulate that in lme but I don't think that makes
610 :     sense. Use the trace of the hat matrix instead.
611 :    
612 : maechler 1271 2006-05-17 Martin Maechler <maechler@stat.math.ethz.ch>
613 :    
614 :     * R/sparseMatrix.R: Matrix <-> graph methods: can no longer use
615 :     the C code depending on a slot structure that's no longer valid.
616 : bates 1352 * src/dgTMatrix.c: ditto (also: src/init.c src/dgTMatrix.h)
617 : maechler 1271
618 :    
619 : bates 1268 2006-05-17 Douglas Bates <bates@stat.wisc.edu>
620 :    
621 :     * R/{AllGeneric.R,Csparse.R},man/band.Rd,NAMESPACE: changed name
622 :     of lowerTriMatrix generic and methods to tril (also upper to triu)
623 :     and added a general band extractor.
624 :    
625 : bates 1267 2006-05-16 Douglas Bates <bates@stat.wisc.edu>
626 :    
627 :     * R/pedigree.R (pedigree): Replace sire and dam values outside the
628 :     allowable range with NAs. Added a corresponding check in the
629 :     validity check for the pedigree class.
630 :    
631 :     * R/[CT]sparse.R ([t]crossprod): The result of single-argument
632 :     crossprod methods now inherits from symmetricMatrix.
633 :    
634 : bates 1265 2006-05-15 Douglas Bates <bates@stat.wisc.edu>
635 :    
636 :     * R/AllGeneric.R (lowerTriMatrix): Added (but did not export)
637 :     generics lowerTriMatrix and upperTriMatrix along with methods for
638 :     the Csparse virtual class. Also added a C function Csparse_band
639 :     that implements these methods by calling cholmod_band.
640 :    
641 : maechler 1264 2006-05-15 Martin Maechler <maechler@stat.math.ethz.ch>
642 :    
643 :     * R/Tsparse.R ("["): column or row subsetting; @Dimnames[k] got
644 :     erased when it was NULL. This led to invalid subselections!
645 :    
646 : bates 1259 2006-04-25 Douglas Bates <bates@stat.wisc.edu>
647 :    
648 :     * R/dtCMatrix.R: avoid coercion of dtCMatrix object to dgCMatrix
649 :     in method for "t" so as not to lose the unit diagonal property.
650 :    
651 : bates 1257 2006-04-19 Douglas Bates <bates@stat.wisc.edu>
652 :    
653 :     * R/lmer.R, R/AllGeneric.R, NAMESPACE: Remove the postVar generic
654 :     and methods. This is now an option to the ranef method for the
655 :     mer class.
656 :    
657 :     * src/cs_utils.c: Ensure that the nz component is -1 for a
658 :     compressed column-oriented matrix. Minor formatting cleanup.
659 :    
660 :     * man/lmer-class.Rd: Document the qqmath method for ranef.lmer
661 :     objects.
662 :    
663 : maechler 1253 2006-04-19 Martin Maechler <maechler@stat.math.ethz.ch>
664 :    
665 :     * R/Auxiliaries.R (diagU2N): new for the solve() methods in
666 :     * R/dtCMatrix.R: where dgC -> dgT coercion now preserves diag = "U".
667 :    
668 : bates 1251 2006-04-15 Douglas Bates <bates@stat.wisc.edu>
669 :    
670 :     * src/cs.[ch],src/cs_utils.[ch] : Added Tim Davis' CSparse library
671 :     in cs.[ch] and utilities to interface to that code in cs_utils.[ch].
672 :    
673 :     * R/dtCMatrix.R, src/dtCMatrix.[ch] : CSparse-based solve methods
674 :     for the dtCMatrix class.
675 : maechler 1253
676 : bates 1247 2006-04-12 Douglas Bates <bates@stat.wisc.edu>
677 :    
678 :     * R/pedigree.R, R/AllClass.R, NAMESPACE: added a pedigree class
679 :     and methods for it.
680 :    
681 : maechler 1245 2006-04-12 Martin Maechler <maechler@stat.math.ethz.ch>
682 :    
683 :     * R/dgCMatrix.R: add storage.mode(.) <- "double" for "matrix"
684 :     arguments, such that M %*% 1:6 now works
685 :     * Tests/matprod.R: test the above
686 :    
687 : bates 1244 2006-04-03 Douglas Bates <bates@stat.wisc.edu>
688 : bates 1243
689 :     * R/lmer.R (qqmath,ranef.lmer-method): added a qqmath method for
690 :     the ranef.lmer class.
691 :    
692 :     * R/AllClass.R, NAMESPACE, R/lmer.R: Added a postVar generic and
693 :     methods to extract the posterior variances from the bVar slot.
694 :    
695 : maechler 1238 2006-03-30 Martin Maechler <maechler@stat.math.ethz.ch>
696 :    
697 :     * R/dtCMatrix.R: allow coercion from dgC* to triangular (dtC*)
698 :     * R/dsCMatrix.R: and symmetric (dsC*) 'Csparse' matrices.
699 :    
700 :     * R/Tsparse.R: Tsparse* -> Csparse* coercion now works and is tested in
701 :     * tests/simple: (extended)
702 :    
703 :     * R/sparseMatrix.R (isTriangular): now using much improved
704 :     * R/Auxiliaries.R (isTriC): new triangularity check for *CMatrix
705 :    
706 : bates 1236 2006-03-23 Douglas Bates <bates@stat.wisc.edu>
707 :    
708 :     * src/dsyMatrix.c (dsyMatrix_as_dspMatrix): Propagate DimNames
709 :     (problem report from Franklin Parlamis). This should be done
710 : maechler 1238 generally.
711 : bates 1236
712 : bates 1234 2006-03-21 Douglas Bates <bates@stat.wisc.edu>
713 :    
714 :     * R/AllClass.R,lmer.R: Change the name of the lmer.ranef class to
715 :     ranef.lmer (like summary.lmer). Add the coef.lmer class and
716 :     update the plot methods.
717 :    
718 : bates 1232 2006-03-20 Douglas Bates <bates@stat.wisc.edu>
719 :    
720 :     * R/lmer.R (resid and ranef methods): Added methods for the
721 :     "residuals" and "resid" generic but only for linear mixed model
722 :     fits. Changed the ranef method to return a list of data frames so
723 :     that the plot methods now work.
724 :    
725 : bates 1230 2006-03-16 Douglas Bates <bates@bates2>
726 :    
727 :     * src/dpoMatrix.c (dpoMatrix_chol): Require n > 0 in call to
728 :     dpotrf - otherwise the BLAS on Mac OS X complains and quits.
729 :    
730 :     * DESCRIPTION (Date): New release
731 :    
732 : maechler 1228 2006-03-15 Martin Maechler <maechler@stat.math.ethz.ch>
733 :    
734 :     * DESCRIPTION (Version): 0.995-6 -- to be released to CRAN
735 :    
736 :     * data/KNex.rda: replacing 'mm' and 'y' by KNex <- list(mm=mm, y=y)
737 :     * man/KNex.Rd: and other help files
738 :     * tests/*.R: several ones needed adaption
739 : bates 1352 * inst/doc/Comparisons.Rnw: ditto
740 : maechler 1228
741 : maechler 1226 2006-03-11 Martin Maechler <maechler@stat.math.ethz.ch>
742 :    
743 :     * R/dgCMatrix.R (replCmat): "[<-" methods for dgCMatrix
744 :    
745 :     * tests/indexing.R: tests for new [<- methods for sparse matrices.
746 :    
747 :     2006-03-10 Martin Maechler <maechler@stat.math.ethz.ch>
748 :    
749 :     * R/dgTMatrix.R (replTmat): "[<-" methods for dgTMatrix
750 :    
751 :     * R/Tsparse.R (.ind.prep): fix out-of-range indexing
752 :    
753 :     2006-03-08 Martin Maechler <maechler@stat.math.ethz.ch>
754 :    
755 :     * R/dMatrix.R: enable things like M [ M < 10 ]
756 :     * R/dgeMatrix.R: implement it
757 :    
758 : maechler 1222 2006-03-06 Martin Maechler <maechler@stat.math.ethz.ch>
759 :    
760 :     * R/AllClass.R: define "summary.mer" and "*.lmer"
761 :     * R/lmer.R (summary): summary(<mer>) computes & returns the above;
762 :     * R/lmer.R (show): now works with summary()
763 :    
764 :     2006-03-04 Martin Maechler <maechler@stat.math.ethz.ch>
765 :    
766 :     * R/dgCMatrix.R: finally direct "Arith" dgC o dgC
767 :     * R/Auxiliaries.R (WhichintersectInd): and other utilities to
768 :     support the above
769 :    
770 : bates 1213 2006-02-07 Douglas Bates <bates@stat.wisc.edu>
771 :    
772 :     * R/lmer.R (lmer): fix initial values of offset and weights for glm.fit.
773 :     Use glmFit$prior.weights for weights in a glmm.
774 :     Allow an option usePQL = FALSE to skip the PQL steps for the
775 :     Laplace method (and, in time, the AGQ method).
776 :    
777 :     * src/lmer.c (mer_factor): Move downdating and factoring of XtX
778 :     into a separate function internal_mer_Xfactor to be able to call
779 :     it from internal_bhat.
780 :    
781 : maechler 1200 2006-01-23 Martin Maechler <maechler@stat.math.ethz.ch>
782 :    
783 :     * tests/Class+Meth.R (tstMatrixClass): function for much better
784 :     testing; now again of all actual classes.
785 :    
786 :     * src/Mutils.c (MAKE_TRIANGULAR_BODY, MAKE_SYMMETRIC_BODY):
787 :     use macros and define make_d_matrix_* and make_i_matrix_*
788 :     where _i_ is for the ldense routines:
789 :    
790 :     * src/ldense.c (ltrMatrix_as_lgeMatrix): provide functions
791 :     * src/ldense.c (lsyMatrix_as_lgeMatrix):
792 :    
793 :     * R/ldenseMatrix.R: use the above in setAs(*,"lgeMatrix")
794 :    
795 :    
796 : maechler 1174 2006-01-16 Martin Maechler <maechler@stat.math.ethz.ch>
797 :    
798 :     * R/Matrix.R (Matrix): has become much "smarter" now auto-producing
799 :     many different kinds of matrices.
800 :     * R/*.R: quite a few new methods were needed for R CMD check with
801 :     new Matrix(). Very good for users playing around.
802 :    
803 :    
804 : maechler 1165 2006-01-15 Martin Maechler <maechler@stat.math.ethz.ch>
805 :    
806 :     * src/dgeMatrix.c (dMatrix_validate): new
807 :     * src/Mutils.c (dense_nonpacked_validate): new
808 :    
809 :     * src/dtrMatrix.c (dtrMatrix_validate): improved/fixed
810 :    
811 :    
812 :     2006-01-14 Douglas Bates <bates@stat.wisc.edu>
813 :    
814 :     * R/AllClass.R (compMatrix), (generalMatrix): new virtual classes
815 :    
816 : bates 1123 2006-01-07 Douglas Bates <bates@stat.wisc.edu>
817 : bates 1119
818 : maechler 1127 * DESCRIPTION (Version): 0.99-6 released to CRAN
819 :    
820 : bates 1119 * src/dgBCMatrix.c (cscb_trcbsm): Fix due to Peter Dalgaard for
821 :     segfault in cases with multiple non-nested grouping factors.
822 :    
823 : maechler 1109 2006-01-03 Martin Maechler <maechler@stat.math.ethz.ch>
824 :    
825 :     * DESCRIPTION (Version): 0.99-4 to be released to CRAN
826 :     (Depends): also on 'utils'
827 :    
828 :     * R/AllClass.R (diagonalMatrix): new class with "ddi*" and "ldi*"
829 :     * R/diagMatrix.R (Diagonal): constructor and methods for
830 :     diagonal matrices
831 :    
832 :     * R/ltTMatrix.R: new "minimal methods"
833 :    
834 : maechler 1091 2005-12-12 Martin Maechler <maechler@stat.math.ethz.ch>
835 :    
836 :     * R/AllGeneric.R (tcrossprod): 2-argument version; here, and for
837 :     all methods (and help files).
838 :    
839 : maechler 1084 2005-12-09 Martin Maechler <maechler@stat.math.ethz.ch>
840 :    
841 :     * R/Auxiliaries.R (dimNamesCheck): fixed thinko -> bug
842 :     for case (dimn. op no_dimn.)
843 :    
844 :     2005-11-14 Douglas Bates <bates@stat.wisc.edu>
845 :    
846 : maechler 1174 * DESCRIPTION (Version): 0.99-2 released to CRAN
847 : maechler 1084
848 : bates 988 2005-10-21 Douglas Bates <bates@stat.wisc.edu>
849 :    
850 :     * R/lmer.R (simulate method): Fixed a drop=FALSE problem reported
851 :     by Julian Faraway.
852 :    
853 : maechler 976 2005-10-06 Martin Maechler <maechler@stat.math.ethz.ch>
854 :    
855 :     * R/Auxiliaries.R (try_as): new utility
856 :     * R/sparseMatrix.R: use try_as() in coercion to original class
857 :    
858 : maechler 956 2005-09-30 Martin Maechler <maechler@stat.math.ethz.ch>
859 :    
860 :     * src/dgCMatrix.c (double_to_csc): and dgeMatrix_to_csc()
861 :    
862 :     2005-09-29 Martin Maechler <maechler@stat.math.ethz.ch>
863 :    
864 :     * R/Auxiliaries.R (dimNamesCheck): added
865 :    
866 :     * R/Matrix.R (as.array), (as.vector): new
867 :    
868 : maechler 954 2005-09-28 Martin Maechler <maechler@stat.math.ethz.ch>
869 :    
870 :     * R/Matrix.R (Matrix): get logical argument 'sparse' with a smart
871 : maechler 956 default.
872 :     * R/AllClass.R: move 'factors' slot toplevel "Matrix";
873 :     "pMatrix" now contains "sparseMatrix"
874 : maechler 954
875 : maechler 948 2005-09-26 Martin Maechler <maechler@stat.math.ethz.ch>
876 :    
877 :     * tests/Class+Meth.R: new tests; t(t(m)) == m
878 :    
879 :     * src/dtCMatrix.c (tsc_transpose): add forgotten "diag" slot
880 :    
881 :     * src/dsTMatrix.c (dsTMatrix_as_dsCMatrix): bad typo (segfault!)
882 :     * src/dtTMatrix.c (dtTMatrix_as_dtCMatrix): new
883 :    
884 :     * R/dspMatrix.R: typo in "t" method
885 :    
886 : maechler 925 2005-09-18 Douglas Bates <bates@wisc.edu>
887 :    
888 :     * R/AllClass.R (TsparseMatrix), CsparseM* and RsparseM*
889 :     * R/Tsparse.R: instead of R/gTMatrix.R
890 :     * R/Csparse.R: new
891 :     * src/Tsparse.c (Tsparse_to_Csparse): new; -> cholmod_()
892 :     * src/Tsparse.c: new; many trivial methods calling cholmod_()
893 :     * src/Csparse.c (Csparse_to_Tsparse), transpose, (mat|cross)prod:
894 :     via cholmod
895 :    
896 :     2005-09-16 Martin Maechler <maechler@stat.math.ethz.ch>
897 :    
898 :     * R/Auxiliaries.R (non0ind): new function using new C code
899 :     * src/dgCMatrix.c (compressed_non_0_ij): new utility
900 :    
901 : bates 917 2005-09-15 Douglas Bates <bates@localhost.localdomain>
902 :    
903 :     * src/chm_common.h: header file required by all C sources that
904 : maechler 1174 call CHOLMOD functions. It defines a cholmod_common structure
905 : bates 917 called 'c' whose address is passed as the last argument to
906 :     (virtually) every CHOLMOD function.
907 :    
908 :     * src/Pattern.c: Simple example of the use of CHOLMOD.
909 :    
910 :     * src/init.c: initialize and finalize the cholmod_common structure.
911 :    
912 :     * src/Makefile: Added source packages CHOLMOD UMFPACK AMD COLAMD
913 :     LDL and CCOLAMD from the U. of Florida sparse matrix library.
914 :    
915 : maechler 908 2005-09-08 Martin Maechler <maechler@stat.math.ethz.ch>
916 :    
917 :     * inst/test-tools.R: new file collecting the utility functions used
918 :     in ./tests/*.R
919 :    
920 :     * R/ddenseMatrix.R (cbind2): new methods for "numeric" and "matrix"
921 :     * R/Matrix.R (cbind2): methods for NULL and missing
922 :    
923 : maechler 886 2005-08-31 Martin Maechler <maechler@stat.math.ethz.ch>
924 :    
925 :     * R/AllClass.R: new "index" class for "[" and "[<-":
926 :     First cut at "symmetricMatrix" and "triangularMatrix"
927 :     * R/gTMatrix.R (.ind.prep): new function;
928 : maechler 1174 Logical and character indexing now work too.
929 : maechler 886 * R/Matrix.R: cheap "[<-" methods for denseMatrix now work
930 :     * tests/indexing.R: new, including *.Rout.save
931 :     * tests/dgTMatrix.R: new
932 :    
933 : bates 876 2005-08-29 Douglas Bates <bates@wisc.edu>
934 :    
935 :     * src/dgTMatrix.c (graphNEL_as_dgTMatrix): Corrected the position
936 :     indicator pos not being updated. Also enforced upper triangular
937 :     for symmetric case. Need to coerce edges component of elements of
938 :     edge list - grr! (Why don't they define their classes cleanly?)
939 :    
940 : maechler 871 2005-08-26 Martin Maechler <maechler@stat.math.ethz.ch>
941 :    
942 :     * R/Matrix.R: added first "[<-" methods; not yet functional
943 : bates 1352 * R/denseMatrix.R: ditto
944 : maechler 871 * man/Subassign-methods.Rd: new help file for these
945 :    
946 :     2005-08-25 Martin Maechler <maechler@stat.math.ethz.ch>
947 :    
948 :     * DESCRIPTION (Version): 0.98-6
949 :    
950 :     * R/denseMatrix.R: new file for "[" fallback methods for all dense
951 :     matrices.
952 :    
953 : maechler 868 2005-08-19 Martin Maechler <maechler@stat.math.ethz.ch>
954 :    
955 :     * src/lgCMatrix.c (lcsc_to_matrix): new; need for
956 :     as( <logical>, "matrix")
957 :    
958 :     * R/pMatrix.R: coercion to "lgTMatrix"
959 :    
960 :     * R/gTMatrix.R: new virtual class to define "[" methods for.
961 :     * man/gTMatrix-class.Rd:
962 :     * General slight re-organization of where "[" methods are defined.
963 :     more to come.
964 :    
965 : maechler 871 2005-08-18 Douglas Bates <bates@wisc.edu>
966 : maechler 868
967 : maechler 1174 * DESCRIPTION (Version): 0.98-5 released to CRAN
968 : maechler 871
969 :     * src/dgTMatrix.c (graphNEL_as_dgTMatrix): add first graphNEL methods
970 :     * .....
971 :    
972 : bates 863 2005-08-18 Douglas Bates <bates@localhost.localdomain>
973 :    
974 :     * R/lmer.R: Corrected naming scheme in mcmcsamp to work with lmer
975 :     or glmer objects.
976 :    
977 : maechler 860 2005-08-17 Martin Maechler <maechler@stat.math.ethz.ch>
978 :    
979 :     * DESCRIPTION (Version): 0.98-4 : upload to CRAN
980 :    
981 :     2005-08-16 Douglas Bates <bates@localhost.localdomain>
982 :    
983 :     * R/HBMM.R: finish re-writing R-only code.
984 :    
985 : bates 854 2005-08-15 Douglas Bates <bates@localhost.localdomain>
986 :    
987 :     * man/externalFormats.Rd: move documentation for writeHB and
988 :     writeMM here.
989 :    
990 :     * src/mmio.c: replace inclusion of <malloc.h> by <stdlib.h>
991 :     (suggested by Paul Roecker).
992 :    
993 :     * tests/validObj.R (assertError): Comment out test that is failing
994 :     after recent changes in r-devel.
995 :    
996 : maechler 860
997 : maechler 848 2005-08-11 Martin Maechler <maechler@stat.math.ethz.ch>
998 :    
999 :     * R/AllClass.R: intermediate virtual class "denseMatrix"
1000 :     * man/denseMatrix-class.Rd
1001 :     * NAMESPACE: export it, and also export
1002 :     * man/unused-classes.Rd: "iMatrix", "zMatrix" and "ldenseMatrix"
1003 :    
1004 : bates 846 2005-08-10 Douglas Bates <bates@wisc.edu>
1005 :    
1006 : maechler 848 * DESCRIPTION (Version): 0.98-3 to CRAN
1007 :    
1008 : bates 846 * src/dtrMatrix.c (dtrMatrix_validate): fixed up validation and
1009 :     matrix_solve code (which was really, really wrong).
1010 :    
1011 : bates 835 2005-08-07 Douglas Bates <bates@wisc.edu>
1012 : maechler 834
1013 :     * DESCRIPTION (Version): 0.98-2
1014 :    
1015 :     * R/HBMM.R (readHB), (readMM): read Matrix Market formats
1016 :    
1017 :     * R/lmer.R (abbrvNms): new
1018 :     * R/lmer.R (mcmcsamp): allow transformed parameters
1019 : bates 835 * src/HBMM.c (Matrix_writeMatrixMarket): Added read/write routines
1020 :     for the Harwell-Boeing and the MatrixMarket formats.
1021 : maechler 834
1022 :     2005-08-04 Martin Maechler <maechler@stat.math.ethz.ch>
1023 :    
1024 :     * man/dtrMatrix-class.Rd: add examples
1025 : bates 835 * man/dtpMatrix-class.Rd: ditto; plus note about PROBLEM
1026 : maechler 834
1027 :     * TODO: note the dtpMatrix (docu) bug
1028 :    
1029 :     * R/zzz.R (.onLoad): assignInNamespace("as.matrix", *, "base")
1030 :     in order to ensure that new as.matrix() is used by old functions,
1031 :     e.g., svd(), qr(), eigen(), dist(),..;
1032 :     apply(), also matplot() or pairs().
1033 :    
1034 :    
1035 :     2005-08-03 Martin Maechler <maechler@stat.math.ethz.ch>
1036 :    
1037 :     * R/lmer.R: add 'fixme' comments and move the linear vs glm check;
1038 :     add comments about 'control' / lmerControl() arguments
1039 :    
1040 : bates 835 2005-07-27 Douglas Bates <bates@wisc.edu>
1041 : bates 820
1042 : bates 835 * man/sleepstudy.Rd: Added the sleep data set.
1043 : maechler 1174 * DESCRIPTION (Version): 0.98-1 released to CRAN
1044 : bates 820
1045 : bates 835 2005-07-12 Douglas Bates <bates@wisc.edu>
1046 : maechler 834 * man/sleepstudy.Rd: Added the sleep data set.
1047 :    
1048 : bates 809 * R/lmer.R (glmmMCMC): Added PACKAGE = "Matrix" in a couple of
1049 :     .Call calls that were producing spurious output.
1050 :    
1051 : bates 835 2005-07-05 Douglas Bates <bates@wisc.edu>
1052 : bates 801
1053 :     * R/lmer.R (lmer): stored updated variance component estimates in
1054 :     mer object for the generalized model. (Bug reported by Renaud
1055 :     Lancelot).
1056 :    
1057 : bates 835 2005-07-03 Douglas Bates <bates@wisc.edu>
1058 : bates 794
1059 :     * src/lmer.c (glmer_devAGQ): Added AGQ for single grouping factor,
1060 :     unidimensional case.
1061 :    
1062 : bates 835 2005-06-08 Douglas Bates <bates@wisc.edu>
1063 : maechler 791
1064 :     * DESCRIPTION (Version): 0.96-1
1065 :    
1066 : maechler 1174 * moved lmer-class' R and C code moved from lme4 to here
1067 : maechler 791
1068 : bates 835 2005-06-04 Douglas Bates <bates@wisc.edu>
1069 : bates 763
1070 :     * R/dgCMatrix.R: Call to csc_matrix_mm used undefined arguments
1071 :     (reported by Guissepe Ragusa <gragusa@ucsd.edu>)
1072 :    
1073 : bates 835 2005-06-02 Douglas Bates <bates@wisc.edu>
1074 : bates 763
1075 :     * src/Makefile.win: Forgot to update this when Makefile changed.
1076 :    
1077 : bates 835 2005-05-11 Douglas Bates <bates@wisc.edu>
1078 : bates 726
1079 :     * src/dgCMatrix.c (csc_transpose): Simplified function fixing a
1080 :     bug reported by Kurt Hornik and Michael Hahsler.
1081 :    
1082 : bates 835 2005-05-10 Douglas Bates <bates@wisc.edu>
1083 : bates 725
1084 :     * src/lgCMatrix.c (Matrix_lgClgCmm): Implementation of methods for
1085 :     logical sparse matrices. These will also be used in the symbolic
1086 :     analysis for lmer objects.
1087 :    
1088 :     * src/dsCMatrix.c (dsCMatrix_matrix_solve): Copied the dimensions
1089 :     of b to the result. Fixes bug reported by Jean.Coursol@math.u-psud.fr
1090 : maechler 791
1091 : bates 835 2005-05-06 Douglas Bates <bates@wisc.edu>
1092 : bates 714
1093 :     * src/dgeMatrix.c (dgeMatrix_colsums): Added an implementation of
1094 :     colMeans, colSums, rowMeans and rowSums.
1095 :    
1096 : bates 835 2005-04-18 Douglas Bates <bates@wisc.edu>
1097 : bates 692
1098 :     * src/lgCMatrix.[ch]: code for _validate method and stub for
1099 :     multiplication operation.
1100 :    
1101 :     * src/dgeMatrix.c (dgeMatrix_matrix_solve): Passing wrong argument
1102 :     to dgetrs.
1103 :    
1104 :     * src/init.c: Fix cut-and-paste error in definition of
1105 :     dgeMatrix_matrix_solve
1106 :    
1107 :     * src/{many files}: Tighten code by using ALLOC_SLOT.
1108 :    
1109 : bates 835 2005-04-15 Douglas Bates <bates@wisc.edu>
1110 : bates 692
1111 :     * R/AllClass.R: Add lgTMatrix and lgCMatrix classes
1112 :    
1113 :     * DESCRIPTION: Eliminate import of stats.
1114 :    
1115 : maechler 791
1116 : bates 835 2005-04-06 Douglas Bates <bates@wisc.edu>
1117 : bates 692
1118 :     * R/AllClass.R : add logical sparse matrix classes
1119 :    
1120 : maechler 687 2005-04-01 Martin Maechler <maechler@stat.math.ethz.ch>
1121 :    
1122 :     * R/dgTMatrix.R: add "[" method for triplet matrices
1123 :     * R/sparseMatrix.R: and other sparse ones; --> add show() for sparse
1124 :    
1125 : bates 835 2005-03-31 Douglas Bates <bates@wisc.edu>
1126 : maechler 687
1127 :     * DESCRIPTION (Version): release 0.95-5 to CRAN
1128 :    
1129 :     * R/dMatrix.R: add %*%, crossprod and solve "fallback" methods
1130 :     * R/sparseMatrix.R: %*%, crossprod()
1131 :     * R/dgeMatrix.R: more "fallback" methods for numeric/dense matrices
1132 :     * man/*.Rd: move method definitions to 'Matrix' and 'dMatrix'
1133 :     * src/lmer.c (lmer_fitted): fix thinko
1134 :    
1135 : maechler 676 2005-03-26 Martin Maechler <maechler@stat.math.ethz.ch>
1136 :    
1137 :     * R/AllClass.R: add two virtual sparse classes ``on top''
1138 :    
1139 :     2005-03-24 Martin Maechler <maechler@stat.math.ethz.ch>
1140 :    
1141 :     * R/AllClass.R (setClass): use "VIRTUAL" for the virtual classes;
1142 :     correspondingly fix examples and tests/ since new()
1143 :     doesn't work for virtual classes.
1144 :    
1145 : maechler 658 2005-03-17 Martin Maechler <maechler@stat.math.ethz.ch>
1146 :    
1147 :     * R/Matrix.R (as.matrix): method and one for unname()
1148 :     * tests/dpoMatrix.R: tests should now be less platform dependent;
1149 :     also run for R 2.1.0; using as.matrix()
1150 :    
1151 : bates 835 2005-03-15 Douglas Bates <bates@wisc.edu>
1152 : maechler 658
1153 :     * R/pMatrix.R: "pMatrix" class added
1154 :     * ....
1155 :    
1156 : bates 835 2005-03-14 Douglas Bates <bates@wisc.edu>
1157 : bates 645
1158 :     * R/dtpMatrix.R: Add unpack method and an example.
1159 :    
1160 :     * src/dsyMatrix.c (dsyMatrix_trf): Add BunchKaufman factorization
1161 :     of general symmetric matrices and associated S4 methods.
1162 :    
1163 : maechler 658 2005-03-10 Martin Maechler <maechler@stat.math.ethz.ch>
1164 :     +
1165 :     2005-03-05 Martin Maechler <maechler@stat.math.ethz.ch>
1166 :    
1167 :     * R/dgeMatrix.R (setAs): and many other files: more coercion,
1168 :     crossprod() and "%*%" methods added; tests, too.
1169 :     * tests/matprod.R: new, for testing these
1170 :    
1171 : bates 835 2005-03-03 Douglas Bates <bates@wisc.edu>
1172 : bates 599
1173 :     * src/lmer.c (lmer_fitted): Added.
1174 :    
1175 : bates 835 2005-03-02 Douglas Bates <bates@wisc.edu>
1176 : bates 596
1177 :     * R/dsTMatrix.R: Conversion from dsTMatrix to dsCMatrix
1178 :    
1179 : bates 835 2005-02-28 Douglas Bates <bates@wisc.edu>
1180 : bates 582
1181 :     * src/*.c,po/,inst/po: Internationalization and localization of
1182 :     the package.
1183 :    
1184 :     * src/ldl.[ch]: Removed these as their contents are referenced in the
1185 :     R_ldl.c file.
1186 :    
1187 :     * src/flame.[ch]: Removed these source files.
1188 : maechler 658
1189 : bates 582 * src/dtrMatrix.c (make_array_triangular): Move to Mutils
1190 :    
1191 :     * src/LU.[ch],src/init.c: absorb in factorizations
1192 :    
1193 :     * src/Mutils.h: prepare for internationalization
1194 :    
1195 :     * src/cblas.h: move the enum definitions to Mutils.h and remove
1196 :     this file
1197 :    
1198 : maechler 578 2005-02-26 Martin Maechler <maechler@stat.math.ethz.ch>
1199 :    
1200 : maechler 579 * R/dgeMatrix.R: provide "dimnames" and "dimnames<-" methods
1201 :    
1202 :     * R/dtrMatrix.R: fix t() method
1203 :    
1204 : maechler 578 * R/dgeMatrix.R: define group methods "Arith", "Math", "Math2"
1205 : maechler 658 * NAMESPACE: export them (and import generics from "methods")
1206 : maechler 578 * tests/group-methods.R : and test them.
1207 :    
1208 :     * src/dtrMatrix.c (dtrMatrix_as_dgeMatrix): prevent seg.fault in
1209 :     border case
1210 :    
1211 :     2005-02-24 Douglas Bates <bates@stat.wisc.edu>
1212 :    
1213 : maechler 658 * DESCRIPTION (Version): 0.95-2 released to CRAN
1214 : maechler 578
1215 :     * src/dgBCMatrix.c:
1216 :     * src/lmer.c: many changes
1217 :     * ...
1218 :    
1219 : maechler 512 2005-02-04 Martin Maechler <maechler@stat.math.ethz.ch>
1220 :    
1221 :     * R/Matrix.R: add more sophisticated show() method.
1222 :    
1223 : maechler 578 2005-02-02 Douglas Bates <bates@stat.wisc.edu>
1224 :    
1225 :     * */* : almost complete reorganization of classes.
1226 :    
1227 : bates 835 2005-01-26 Douglas Bates <bates@wisc.edu>
1228 : bates 460
1229 :     * R/AllGeneric.R: Added matrix exponential generic expm and a method
1230 :     for the geMatrix class.
1231 :    
1232 : bates 835 2005-01-24 Douglas Bates <bates@wisc.edu>
1233 : bates 460
1234 :     * src/Makefile (clean): Remove *.a and *.so
1235 :    
1236 :     * man/cscBlocked-class.Rd: Remove reference to the lmer-class.
1237 :    
1238 : bates 835 2005-01-23 Douglas Bates <bates@wisc.edu>
1239 : bates 460
1240 : maechler 658 * src/lmer.c (Lind): Definition of Lind was backwards. This only
1241 : bates 460 had an effect in cases with more than 2 grouping factors.
1242 :    
1243 : bates 835 2005-01-03 Douglas Bates <bates@wisc.edu>
1244 : bates 415
1245 :     * src/lmeRep.c (lmer_variances): change from lmeRep to lmer
1246 :    
1247 : bates 835 2004-12-23 Douglas Bates <bates@wisc.edu>
1248 : bates 410
1249 :     * src/init.c (R_init_Matrix): Reorder calls to R_registerRoutines
1250 :     and R_useDynamicSymbols (suggested by B.D.Ripley).
1251 :    
1252 : bates 835 2004-12-14 Douglas Bates <bates@wisc.edu>
1253 : bates 392
1254 :     * R/sscMatrix.R: Add determinant methods
1255 :    
1256 :     * src/triplet.[ch],src/init.c (triplet_to_matrix): Add a coercion
1257 :     for tripletMatrix to matrix.
1258 :    
1259 : bates 835 2004-12-13 Douglas Bates <bates@wisc.edu>
1260 : bates 388
1261 : bates 392 * R/AllClass.R (.onLoad): Eliminate the bbCrosstab class, which is
1262 :     no longer used.
1263 :    
1264 : bates 388 * src/R_ldl.c: Created an R-specific version of the ldl.[ch] files
1265 :     with dynamic allocation of scratch arrays.
1266 :    
1267 :     * src/ssclme.c (ssclme_copy_ctab): Fixed bug in creation of ZtZ
1268 :     for multivariate random effects with multiple grouping factors.
1269 :     Fixes part but not all of #15.
1270 :    
1271 : bates 835 2004-12-03 Douglas Bates <bates@wisc.edu>
1272 : bates 375
1273 :     * src/lmeRep.c (lmeRep_factor): order of operations for multiple
1274 :     scalar grouping factors corrected.
1275 :    
1276 : bates 835 2004-11-29 Douglas Bates <bates@wisc.edu>
1277 : bates 375
1278 :     * src/bCrosstab.c: remove diag_update which is no longer used
1279 :    
1280 : bates 835 2004-11-16 Douglas Bates <bates@wisc.edu>
1281 : bates 350
1282 :     * src/Metis_utils.c: Move metis.h include to C sources so that the
1283 :     .h file can be included.
1284 :    
1285 : bates 835 2004-11-12 Douglas Bates <bates@wisc.edu>
1286 : bates 342
1287 : bates 350 * src/LU.c,geMatrix.c,trMatrix.c, etc.:
1288 : bates 342 Complete allocation of slots in NEW_OBJECT.
1289 :    
1290 :     * src/Mutils.h: Moved list of symbols to an include file
1291 :    
1292 : bates 835 2004-11-11 Douglas Bates <bates@wisc.edu>
1293 : bates 342
1294 :     * src/geMutils.c (Matrix_init): remove unused function
1295 :    
1296 : bates 835 2004-11-10 Douglas Bates <bates@wisc.edu>
1297 : bates 342
1298 :     * src/cscMatrix.c (csc_to_imagemat): removed unused function
1299 :    
1300 : bates 835 2004-11-05 Douglas Bates <bates@wisc.edu>
1301 : bates 327
1302 :     * src/Makefile.win (SOURCES_C): Keep consistent with Makefile
1303 :    
1304 : bates 835 2004-10-27 Douglas Bates <bates@wisc.edu>
1305 : bates 303
1306 :     * R/pdmatrix.R: remove PACKAGE="Matrix" in .Call calls
1307 :    
1308 : bates 835 2004-10-04 Douglas Bates <bates@wisc.edu>
1309 : bates 296
1310 :     * src/init.c: Created R_init_Matrix and added registration of C
1311 :     routines.
1312 :    
1313 : bates 835 2004-10-02 Douglas Bates <bates@wisc.edu>
1314 : bates 283
1315 :     * R/tripletMatrix.R: Force a require(lattice) for the image methods.
1316 :    
1317 : bates 835 2004-06-15 Douglas Bates <bates@wisc.edu>
1318 : bates 229
1319 :     * man/trMatrix-class.Rd: Escape the % chars in .Rd files.
1320 :    
1321 : bates 111 2004-04-20 Douglas Bates <bates@stat.wisc.edu>
1322 :    
1323 :     * src/Makefile.win ($(SHLIB)): Modifications per Uwe Ligges.
1324 :    
1325 : bates 109 2004-04-19 Douglas Bates <bates@stat.wisc.edu>
1326 :    
1327 :     * src/ssclme.c (ssclme_update_mm): fix logic error in
1328 :     ssclme_update_mm
1329 :    
1330 : bates 105 2004-04-18 Douglas Bates <bates@stat.wisc.edu>
1331 :    
1332 :     * src/ssclme.c (ssclme_coef, ssclme_coefGets): Create consistency
1333 :     in the order of unconstrained and constrained parameters.
1334 :     (ssclme_gradient): Added the gradients (not yet correct for
1335 :     multidimensional, unconstrained case).
1336 :    
1337 : bates 78 2004-04-14 Douglas Bates <bates@stat.wisc.edu>
1338 :    
1339 :     * src/ssclme.c (ssclme_EMsteps): Fix logic in REML update
1340 :    
1341 :     * src/Makefile.win: Remove unneeded ranlib call
1342 :    
1343 : bates 71 2004-04-12 Douglas Bates <bates@stat.wisc.edu>
1344 :    
1345 :     * DESCRIPTION (Version): New release
1346 :    
1347 :     * src/Makefile.win: Update Makefile.win to umfpack removal.
1348 :    
1349 : bates 49 2004-04-05 Douglas Bates <bates@bates2_home>
1350 :    
1351 :     * src/triplet_to_col.c: Create triplet_to_col as a native
1352 : maechler 658 function, not the version from umfpack. There were problems with
1353 : bates 49 the configuration of UMFPACK for 64-bit processors and there was
1354 :     only one umfpack routine being used so I moved it here.
1355 :    
1356 : bates 45 2004-04-04 Douglas Bates <bates@bates2_home>
1357 :    
1358 :     * src/ssclme.c (ssclme_variances): New function.
1359 :    
1360 : bates 28 2004-03-28 Douglas Bates <bates@bates2_home>
1361 :    
1362 :     * src/ssclme.c (ssclme_fitted): Added function.
1363 :    
1364 : bates 22 2004-03-27 Douglas Bates <bates@bates2_home>
1365 :    
1366 :     * src/ssclme.c (ssclme_transfer_dimnames): Add new function to
1367 :     store the dimnames in the XtX and bVar slots
1368 :     (ssclme_update_mm): Change the dimensions of the bVar slot
1369 :     components and the returned value from ssclme_ranef.
1370 :    
1371 : bates 10 2004-03-18 Douglas Bates <bates@stat.wisc.edu>
1372 :    
1373 :     * R/{pdMat.R,pdIdent.R,pdLogChol.R,pdMatrixLog.R,pdNatural.R},
1374 :     src/{pdMat.c,pdIdent.c,pdLogChol.c,pdNatural.c},
1375 :     tests/{pdCompSymm.R,pdDiag.R,pdIdent.R,pdLogChol.R,pdNatural.R},
1376 :     man/{pdMat-class.Rd,pdmatrix-class.Rd,corrmatrix-class.Rd,
1377 :     pdDiag-class.Rd,pdIdent-class.Rd,pdNatural-class.Rd,
1378 :     pdLogChol-class.Rd,coefGets.Rd,pdCompSymm-class.Rd,
1379 :     pdfactor-class.Rd,pdFactor.Rd,pdMatrix.Rd,
1380 :     pdBlocked-class.Rd},AllClass.R,AllGeneric.R:
1381 :     Moved the pdMat classes from the lme4 package.
1382 :    
1383 :     2004-03-02 Douglas Bates <bates@stat.wisc.edu>
1384 :    
1385 :     * man/ssclme-class.Rd: Update definition and documentation of the
1386 :     ssclme class to include the DIsqrt slot.
1387 :    
1388 :     * src/ssclme.c (ssclme_deviance): Modify order of computation
1389 :     (much faster using dsyrk, a level 3 BLAS routine).
1390 :    
1391 :     * src/Makefile (SUBLIBS): Change definition (K. Hornik)
1392 :    
1393 :     2004-02-28 Douglas Bates <bates@stat.wisc.edu>
1394 :    
1395 :     * tests/ssclme.R: Modify the test to account for the permutation
1396 :     of the levels of the grouping factors.
1397 :    
1398 :     2004-02-23 Douglas Bates <bates@stat.wisc.edu>
1399 :    
1400 :     * R/ssclme.R,src/ssclme.c (ssclme): Move slots of sscCrosstab slot
1401 :     directly into the ssclme class definition.
1402 :    
1403 :     2004-02-22 Douglas Bates <bates@stat.wisc.edu>
1404 :    
1405 :     * DESCRIPTION (Date): New release
1406 :    
1407 :     * man/ssclme-class.Rd: new file.
1408 :    
1409 :     * src/ssclme.c (ssclme_loglik): major revisions in design. It
1410 :     works and it's fast!
1411 :    
1412 :     2004-02-17 Douglas Bates <bates@stat.wisc.edu>
1413 :    
1414 :     * src/taucs/Makefile.win (lib): Change "ar" to "$(AR)" (B.Ripley)
1415 :    
1416 :     2004-02-16 Douglas Bates <bates@stat.wisc.edu>
1417 :    
1418 :     * DESCRIPTION (Date): New release
1419 :    
1420 :     * NAMESPACE: Don't export ssclme.
1421 :    
1422 :     * data/ScotsSec.rda, man/ScotsSec.Rd: Add Scottish secondary
1423 :     school data.
1424 :    
1425 :     2004-02-11 Douglas Bates <bates@stat.wisc.edu>
1426 :    
1427 :     * src/sscCrosstab.c (sscCrosstab): Added a row to the incidence to
1428 :     keep track of the fixed-effects and the response. Counts also
1429 :     gets an extra element, which is always one.
1430 :    
1431 :     * src/ldl.c: Include these routines from Tim Davis' LDL package.
1432 :    
1433 :     2004-02-10 Douglas Bates <bates@stat.wisc.edu>
1434 :    
1435 :     * src/cscMatrix.c (csc_transpose): new function
1436 :    
1437 :     * src/Mutils.c (csc_sort_columns): perm/iperm confusion corrected
1438 :     (csc_components_transpose): new function
1439 :    
1440 :     2004-02-06 Douglas Bates <bates@stat.wisc.edu>
1441 :    
1442 :     * src/triplet.c (triplet_validate): Fix Dim slot on generated
1443 :     triplets
1444 :    
1445 :     2004-01-30 Douglas Bates <bates@stat.wisc.edu>
1446 :    
1447 :     * R/sscCrosstab.R (sscCrosstab): Added sscCrosstab generator function.
1448 :    
1449 :     * src/LU.h (MATRIX_LU_H): Add #ifndef #define ... #endif to this
1450 :     and all other .h files in src.
1451 :    
1452 :     * src/Makefile.win: This and other Makefile.win files contributed
1453 :     by Brian Ripley.
1454 :    
1455 :     2004-01-27 Douglas Bates <bates@stat.wisc.edu>
1456 :    
1457 :     * R/syMatrix.R: Added methods for "%*%".
1458 :    
1459 :     * R/Hilbert.R (Hilbert): Changed Hilbert function to return a
1460 :     poMatrix object.
1461 :    
1462 :     2004-01-26 Douglas Bates <bates@stat.wisc.edu>
1463 :    
1464 :     * man/sscChol-class.Rd,man/mm.Rd,man/y.Rd: Added man pages.
1465 :    
1466 :     2004-01-25 Douglas Bates <bates@bates2_home>
1467 :    
1468 :     * inst/doc/Introduction.Rnw,Comparisons.Rnw: Added vignettes.
1469 :    
1470 :     * R/csc.R: Convert all cscMatrix classes to use Dim slot instead
1471 :     of nrow.
1472 :    
1473 :     2003-12-31 Douglas Bates <bates@stat.wisc.edu>
1474 :    
1475 :     * src/taucs/taucs.h: Moved taucs.h, amd.h, and umfpack.h into
1476 :     subdirectories.
1477 :    
1478 :     2003-12-08 Douglas Bates <bates@stat.wisc.edu>
1479 :    
1480 :     * src/taucs.h: Accidently referred to global header files
1481 :     instead of local files.
1482 :    
1483 :     2003-12-04 Douglas Bates <bates@stat.wisc.edu>
1484 :    
1485 :     * R/AllClass.R: Lots of changes. Removed all the lapack++ code
1486 :     and methods and replaced all classes with S4 classes.
1487 :    
1488 :     2003-04-19 Douglas Bates <bates@stat.wisc.edu>
1489 :    
1490 :     * R/det.R,man/det.Rd: Change name of det generic to determinant
1491 :    
1492 :     * src/R_LapackPP.cc: Change method of calculating determinants
1493 :    
1494 :     2003-02-03 Douglas Bates <bates@stat.wisc.edu>
1495 :    
1496 :     * DESCRIPTION (Version): removed empty data directory as requested
1497 :     by CRAN maintainers. Changed version number and date.
1498 :    
1499 :     2002-10-23 Douglas Bates <bates@stat.wisc.edu>
1500 :    
1501 :     * src/laindex.h: Applied patches from Brian Ripley for compilation
1502 :     under Windows.
1503 :    
1504 :     * Added configure.win and src/Makevars.win as requested by Brian
1505 :     Ripley.
1506 :    
1507 :     2002-05-03 Douglas Bates <bates@stat.wisc.edu>
1508 :    
1509 :     * src/lamatrix.h: Removing pre-1.2.0 compatibility code per Kurt
1510 :     Hornik.
1511 :    
1512 :     2002-04-24 Douglas Bates <bates@stat.wisc.edu>
1513 :    
1514 :     * configure.ac: Replaced configure.in with configure.ac
1515 :     contributed by Kurt Hornik.
1516 :    
1517 :     * aclocal.m4 (ac_clean_files): Replaced this with Kurt Hornik's
1518 :     version for R-1.5.0
1519 :    
1520 : maechler 512
1521 : bates 10 2001-12-10 Douglas Bates <bates@stat.wisc.edu>
1522 :    
1523 :     * man/eigen.Rd: Removed the .Alias in the example

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