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Annotation of /pkg/ChangeLog

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

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