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Annotation of /pkg/ChangeLog

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1 : maechler 1647 2006-10-23 Martin Maechler <maechler@stat.math.ethz.ch>
2 :    
3 :     * DESCRIPTION (Version): 0.9975-5 ready for release
4 :    
5 : bates 1646 2006-10-20 Douglas Bates <bates@stat.wisc.edu>
6 :    
7 :     * src/init.c (R_init_Matrix): export more cholmod CCallable functions.
8 :    
9 : maechler 1642 2006-10-20 Martin Maechler <maechler@stat.math.ethz.ch>
10 :    
11 :     * R/AllClass.R (corMatrix): add 'validity' check;
12 :     comment out unused "LDL" class definition
13 :     * NAMESPACE: mention, but do not export "LDL" class
14 :     * R/corMatrix.R: new (simple), needed for R-devel with
15 :     * tests/Class+Meth.R (tstMatrixClass): 1 exception for corMatrix
16 :     coerce and t() exceptions for all 5 'Mat.MatFact' classes.
17 :    
18 : bates 1641 2006-10-19 Douglas Bates <bates@stat.wisc.edu>
19 :    
20 :     * src/chm_common.h: Add R_cholmod_start to initialize cholmod to
21 :     use Rprintf and R's error handling.
22 :    
23 : maechler 1635 2006-10-17 Martin Maechler <maechler@stat.math.ethz.ch>
24 :    
25 :     * R/diagMatrix.R (%*%): rep(*, each = .) in Matrix %*% diagonal.
26 :     * tests/matprod.R: add tests for the bug fixed.
27 :    
28 : bates 1624 2006-10-11 Douglas Bates <bates@stat.wisc.edu>
29 :    
30 :     * src/HBMM.[ch]: remove HarwellBoeing format for writing.
31 :     * src/SOURCES_C.mkf (SOURCES_C): no longer compile iohb.c
32 :    
33 :     2006-10-06 Douglas Bates <bates@stat.wisc.edu>
34 :    
35 : bates 1629 * R/d[gs]CMatrix.R: deprecate the writeHB function. Use writeMM instead.
36 : bates 1624
37 : maechler 1618 2006-10-06 Martin Maechler <maechler@stat.math.ethz.ch>
38 :    
39 :     * DESCRIPTION (Version): 0.9975-3
40 :    
41 :     * R/diagMatrix.R (bdiag): new function constructing block diagonal
42 :     (sparse) matrices.
43 :     * man/bdiag.Rd: docu + examples
44 :    
45 : maechler 1619 * R/Csparse.R (replCmat): calling new Csparse_drop() now.
46 :    
47 : maechler 1618 * src/Csparse.c (Csparse_general_to_symmetric, Csparse_drop): new functions
48 :     * R/lsCMatrix.R: three more coercions to lsC (thanks to the above)
49 :    
50 :     * R/diagMatrix.R (Diagonal): '[<-' method for diag.matrices such
51 :     that result is sparse or diagonal (and not dense).
52 :    
53 :     * man/Subassign-methods.Rd: fix examples
54 :    
55 :     * R/Matrix.R (Matrix): Matrix(0, *) or Matrix(*, sparse=TRUE)
56 :     should always return a sparse (and not sometimes a diagonal) matrix.
57 :    
58 : maechler 1615 2006-10-05 Martin Maechler <maechler@stat.math.ethz.ch>
59 :    
60 :     * R/Matrix.R ([<-): also for value "Matrix" or "matrix"
61 :    
62 : bates 1613 2006-10-04 Douglas Bates <bates@stat.wisc.edu>
63 :    
64 :     * DESCRIPTION (Version): 0.9975-2
65 : maechler 1615
66 : bates 1613 * inst/include/Matrix_stubs.c (M_cholmod_sparse_to_triplet): export more symbols
67 :    
68 : bates 1611 2006-10-02 Douglas Bates <bates@R-project.org>
69 :    
70 :     * tests/dg_Matrix.R: Simplify test taking into account new code.
71 :    
72 : maechler 1599 2006-09-29 Martin Maechler <maechler@stat.math.ethz.ch>
73 :    
74 : maechler 1600 * R/Csparse.R (replCmat): improve for missing i / j in non-simple cases
75 :    
76 : maechler 1599 * R/lsTMatrix.R: new files w/ missing methods
77 :     * R/nsTMatrix.R: " 'for completeness'
78 :    
79 :     * tests/Class+Meth.R: a bit less 'not.ok.classes'
80 :    
81 :     * R/Tsparse.R (t): generalized "t" method from "dgT*" to "Tsparse*"
82 :    
83 :    
84 : bates 1595 2006-09-28 Douglas Bates <bates@R-project.org>
85 :    
86 :     * src/dppMatrix.h: Ensure definition of dspMatrix_validate is
87 :     included.
88 :    
89 :     * src/init.c, inst/include/{Matrix.h,Matrix_stubs.h,cholmod.h}:
90 :     Export C-callable functions used in Zt_create in lme4.
91 :    
92 : maechler 1592 2006-09-28 Martin Maechler <maechler@stat.math.ethz.ch>
93 :    
94 :     * DESCRIPTION (Version): 0.9975-1
95 :    
96 :     * tests/simple.R: less checks fail; using NA, found that our
97 :     kronecker() is not base-compatible with NA's.
98 :    
99 :     * R/dMatrix.R: "Compare" method now implemented for all cases
100 :    
101 :     * R/Auxiliaries.R (indTri): == which([lower/upper].tri( * )) new utility
102 :    
103 :     * man/dtpMatrix-class.Rd: mention length of 'x' slot
104 :    
105 :     * src/dtpMatrix.c (dtpMatrix_validate): fix check
106 :     * src/dspMatrix.c (dspMatrix_validate): ditto
107 :    
108 :     * R/dtTMatrix.R (gt2tT): fix ("l" -> "n")
109 :     including coercion to [nl]tTMatrix.
110 :    
111 :     * R/diagMatrix.R (show): print a header line as for other classes.
112 :    
113 :     2006-09-27 Martin Maechler <maechler@stat.math.ethz.ch>
114 :    
115 :     * src/Makefile.win (SUBDIRS): fix typo
116 :    
117 : maechler 1583 2006-09-19 Martin Maechler <maechler@stat.math.ethz.ch>
118 :    
119 :     * DESCRIPTION (Date): ready to release 0.9975-0 to CRAN
120 :    
121 : bates 1577 2006-09-18 Douglas Bates <bates@stat.wisc.edu>
122 :    
123 :     * R/[CT]sparse.R (crossprod and tcrossprod): Handle the cases for x
124 :     symmetric and y missing in R code using %*% (cholmod_aat doesn't
125 :     accept a symmetric matrix).
126 :     * tests/group-methods.R: Uncomment test of crossprod applied to
127 :     lsCMatrix objects.
128 :    
129 : maechler 1575 2006-09-18 Martin Maechler <maechler@stat.math.ethz.ch>
130 :    
131 :     * R/AllClass.R (symmetricMatrix): add validity method (available
132 :     in C for a long time). Many "n..Matrix": drop (wrong) validity arg.
133 :    
134 :     * src/lgCMatrix.c (lgCMatrix_validate): check 'x' slot (!)
135 :    
136 :     * tests/indexing.Rout.save:
137 :     * tests/indexing.R: additions, mainly for 'lsparse'
138 :    
139 :     * R/diagMatrix.R (Diagonal) & coercion to lgTMatrix: fixes for NA
140 :     case.
141 :    
142 :     * R/Auxiliaries.R (nz.NA): new utility now used in nnzero()
143 :    
144 : maechler 1571 2006-09-16 Martin Maechler <maechler@stat.math.ethz.ch>
145 :    
146 : maechler 1572 * R/sparseMatrix.R (prSpMatrix): print logical NAs "visibly"
147 :     as 'N' (1-letter - Ok?)
148 :    
149 : maechler 1571 * tests/group-methods.R: add test for logical + NAs
150 :    
151 :     * R/dMatrix.R ("Compare"): fix to work with NA's
152 :    
153 :     * R/AllClass.R: "Cholesky" etc now inherit from MatrixFactorization.
154 :    
155 :     * src/lgCMatrix.c (ncsc_to_matrix): renamed from lcsc_to_matrix()
156 :     which is implemented.
157 :    
158 : maechler 1565 2006-09-15 Martin Maechler <maechler@stat.math.ethz.ch>
159 :    
160 : maechler 1571 * src/chm_common.c: coerce logical <-> double instead of
161 :     typecasting; needed for "l" matrix handling in cholmod.
162 : maechler 1565
163 : maechler 1571 * tests/other-pkgs.R (graph): small extension in "graph" checks.
164 :    
165 : maechler 1565 * R/sparseMatrix.R (graphNEL -> Tsparse): method for weight case.
166 :     (Tsp2grNEL): other fixes needed
167 :    
168 : maechler 1548 2006-09-11 Martin Maechler <maechler@stat.math.ethz.ch>
169 :    
170 :     * R/AllClass.R ("nMatrix"): and subclasses for "nonzero pattern"
171 :     Matrices, since "lMatrix", also "lsparseM" can have NA
172 :     * R/ndenseMatrix.R, etc: new source files
173 :     * man/nsparseMatrix-classes.Rd, etc: new help files
174 :     * tests/: adaptions
175 :     * src/chm_common.c (chm_dense_to_SEXP): and others:
176 :     new 'Rkind' argument: "l*" and "d*" both use CHOLMOD_REAL
177 : maechler 1582 * src/Csparse.c, etc: ditto
178 : maechler 1548
179 : bates 1546 2006-09-11 Douglas Bates <bates@R-project.org>
180 :    
181 :     * src/Mutils.[ch],init.c inst/include/*.h: Move the
182 :     alloc_d**Matrix functions to the lme4 package.
183 :    
184 : bates 1543 2006-09-09 Douglas Bates <bates@R-project.org>
185 :    
186 :     * src/dsCMatrix.c (dsCMatrix_Cholesky): igoring LDL = FALSE now
187 : maechler 1544 fixed
188 : bates 1543
189 : maechler 1544 2006-09-09 Martin Maechler <maechler@stat.math.ethz.ch>
190 :    
191 : maechler 1548 * R/lMatrix.R: new
192 :    
193 : maechler 1544 * R/sparseMatrix.R (Tsp2grNEL): do not yet use graph::foo()
194 :    
195 :     * R/dgeMatrix.R: do not define tcrossprod() methods for "matrix"
196 : maechler 1582 * man/tcrossprod.Rd: ditto
197 : maechler 1544
198 : bates 1538 2006-09-08 Douglas Bates <bates@stat.wisc.edu>
199 :    
200 :     * inst/include/Matrix_stubs.c,Matrix.h: Add declarations and stubs
201 :     for exported functions
202 :     * src/Makefile, src/CHOLMOD/Lib/Makefile, src/Metis,CAMD,CCOLAMD:
203 :     Remove partitioning algorithms for sparse matrix reordering. The
204 :     copyright on the Metis code was problematic and the methods were
205 :     rarely used.
206 :     * src/triplet_to_col.[ch],MMHB.[ch]: Remove triplet_to_col. Such
207 :     operations are now done entirely in CHOLMOD code.
208 :    
209 : bates 1517 2006-09-06 Douglas Bates <bates@R-project.org>
210 :    
211 :     * src/Mutils.h: Remove functions that are no longer used.
212 :    
213 : bates 1507 2006-09-04 Douglas Bates <bates@R-project.org>
214 :    
215 :     * src/dtCMatrix.c (dtCMatrix_validate): rename functions.
216 :     * src/DEPS.mkf: update
217 :    
218 : maechler 1481 2006-09-02 Martin Maechler <maechler@stat.math.ethz.ch>
219 :    
220 :     * created branches/Matrix-for-R-2.3.x; on trunk: do
221 :     * DESCRIPTION (Version): 0.9975-0
222 :     (Depends): R (>= 2.4.0)
223 :    
224 : bates 1475 2006-09-01 Douglas Bates <bates@R-project.org>
225 :    
226 :     * R/sparseMatrix.R: Added direct method to CsparseMatrix from graphNEL
227 :    
228 : maechler 1472 2006-09-01 Martin Maechler <maechler@stat.math.ethz.ch>
229 :    
230 :     * R/sparseMatrix.R: add coercion from "ANY" to "sparseMatrix"
231 :     * R/denseMatrix.R: add coercion from "ANY" to "denseMatrix"
232 :    
233 :     * R/Matrix.R ([): use nargs() to disambiguate M[i] and M[i,]
234 :    
235 :     2006-08-31 Martin Maechler <maechler@stat.math.ethz.ch>
236 :    
237 :     * R/sparseMatrix.R (Arith): moved Arith group method one-level up
238 :     from "dsparse" to "sparse" and now go via "Csparse" instead of "dgC"
239 : maechler 1582 * R/dsparseMatrix.R: ditto
240 :     * R/Csparse.R: ditto
241 : maechler 1472
242 :     2006-08-31 Martin Maechler <maechler@stat.math.ethz.ch>
243 :    
244 :     * R/dMatrix.R (Compare): improve availability of "<", etc
245 :     * R/Auxiliaries.R (asTuniq): new; also make use of R 2.4.x print(*,max)
246 :    
247 : maechler 1467 2006-08-30 Martin Maechler <maechler@stat.math.ethz.ch>
248 :    
249 :     * R/dgCMatrix.R: aargh: "Arith(<dgC>, numeric)" was wrong because
250 :     of a 0-index which was used as 1-index (..hmm)
251 :    
252 :     * R/sparseMatrix.R (prSpMatrix): fix printing an all-0 sparse Matrix
253 :    
254 :     * R/Auxiliaries.R (all0, is0): for 0-testing in presence of NA's
255 :     * R/Auxiliaries.R (isTriMat): use all0() for 0-testing.
256 : maechler 1582 (.is.diagonal): ditto
257 : maechler 1467
258 :     * R/lgTMatrix.R: as("matrix", "lgTMatrix"): warn about NA's
259 :    
260 :     * R/Matrix.R (Matrix): also work for NA data
261 :    
262 : maechler 1455 2006-08-28 Martin Maechler <maechler@stat.math.ethz.ch>
263 :    
264 :     * R/Matrix.R (Matrix): + 'forceCheck' argument; dimnames setting
265 :     in all cases.
266 :    
267 : bates 1453 2006-08-27 Douglas Bates <bates@R-project.org>
268 :    
269 :     * src/dense.[ch],init.c, R/ddenseMatrix.R, man/band.Rd
270 :     (ddense_band): Added triu, tril and band for ddenseMatrix objects.
271 :    
272 : maechler 1447 2006-08-25 Martin Maechler <maechler@stat.math.ethz.ch>
273 :    
274 :     * src/Mutils.c (dup_mMatrix_as_dgeMatrix): added all subclasses of
275 :     subclasses of "ddenseMatrix"
276 :     * src/init.c et al: outcomment dtrM*_as_dge* and dsyM*_as_dge*_
277 :     * R/ddenseMatrix.R et al: setAs("ddenseMatrix", "dgeMatrix", ..)
278 :     instead of half dozen specialized ones.
279 :    
280 : bates 1445 2006-08-25 Douglas Bates <bates@R-project.org>
281 :    
282 :     * R/lmer.R (qqmath method): Bug fix provided by Emmanuel Tillard
283 :     <tillard@cirad.fr> - ordering standard errors to match effects.
284 :    
285 : bates 1439 2006-08-24 Douglas Bates <bates@R-project.org>
286 : bates 1431
287 : bates 1439 * src/lsCMatrix.c (lsCMatrix_trans): Remove lsCMatrix_chol based
288 :     on R_ldl.
289 :     * R/lCholCMatrix.R,
290 :     src/[dl]CholCMatrix.[ch],R_ldl.[ch],Metis_utils.[ch]: removed
291 :     * src/dsCMatrix.c (dsCMatrix_to_dgTMatrix): use CHOLMOD
292 :     * many files in ./R and ./src: Use more general version of
293 :     dup_mMatrix_as_dgeMatrix to simplify method definitions.
294 : bates 1442 * src/Mutils.c (dup_mMatrix_as_dgeMatrix): Add ddiMatrix,
295 :     dtpMatrix, dspMatrix and dppMatrix conversions.
296 :    
297 : maechler 1447
298 : bates 1439 2006-08-23 Douglas Bates <bates@R-project.org>
299 :    
300 :     * R/AllClass.R,lCholCMatrix.R,src/SOURCES_C.mkf,init.c,NAMESPACE:
301 :     Remove classes lCholCMatrix and dCholCMatrix based on R_ldl code.
302 : bates 1431 * src/dgeMatrix.c: Ensure 'factors' slot exists in result of
303 :     dgeMatrix_crossprod (may need to do this in other places).
304 :     * R/AllGeneric.R,dsCMatrix.R, src/dscMatrix.[ch]: Add Cholesky
305 :     generic and method for dsCMatrix. Use CHOLMOD for chol().
306 :    
307 : bates 1414 2006-08-22 Douglas Bates <bates@R-project.org>
308 :    
309 :     * src/Mutils.c (dup_mMatrix_as_dgeMatrix): updated for general
310 :     types of classed Matrices, matrices or numeric or logical vectors.
311 : bates 1423 * src/init.c: register dup_mMatrix_as_dgeMatrix for coercions.
312 :     * src/chm_common.c,Mutils.h (as_cholmod_factor): Move check_class
313 :     to Mutils.h (as an inline) and change name to Matrix_check_class;
314 :     fixes in as_cholmod_factor and chm_factor_to_SEXP.
315 :     * src/dsCMatrix.[ch]: Use CHOLMOD for dsCMatrix_chol and
316 :     dsCMatrix_matrix_solve. Comment out vestigial functions.
317 :     * src/Csparse.c: use diag_P and uplo_P macros.
318 : maechler 1447
319 : bates 1405 2006-08-21 Douglas Bates <bates@R-project.org>
320 :    
321 :     * src/lmer.c (internal_mer_RZXinv): Fix memory leak caught by
322 : maechler 1447 valgrind.
323 : bates 1411 * tests/matprod.R: Add tests to verify that 'solve' and '%*%' are
324 :     inverses.
325 :     * src/sparseQR.c (sparseQR_validate): add new validation test, fix
326 :     -Wall warnings.
327 :     * src/dppMatrix.c,dtrMatrix.c,dgCMatrix.c,dgeMatrix.c,dspMatrix.c:
328 :     Use dup_mMatrix_as_dgeMatrix.
329 : maechler 1447
330 : bates 1403 2006-08-20 Douglas Bates <bates@R-project.org>
331 :    
332 :     * src/sparseQR.c: Fix thinko in sparseQR_resid_fitted.
333 :     * tests/sparseQR.R: Added
334 :     * man/sparseQR-class.Rd: Document methods for qr.* generics
335 :     * R/sparseQR.R: Return correct # of coefs; fix cut-and-paste errors
336 :    
337 : bates 1398 2006-08-19 Douglas Bates <bates@R-project.org>
338 :    
339 :     * NAMESPACE, R/sparseQR.R, src/init.c,sparseQR.[ch],SOURCES_C.mkf:
340 :     Added methods for sparseQR for qr.qy, qr.qty, qr.coef, qr.resid
341 :     and qr.fitted.
342 :     * src/Mutils.[ch]: Added dup_mMatrix_as_dgeMatrix utility
343 :     * src/dgCMatrix.c: Check for ordering before storing q in dgCMatrix_QR
344 :    
345 : maechler 1389 2006-08-18 Martin Maechler <maechler@stat.math.ethz.ch>
346 :    
347 :     * R/AllGeneric.R: add "qr" and "chol" generics; via 'trick' since
348 :     the base version has no "..." argument.
349 :    
350 :     * R/sparseMatrix.R (prSpMatrix): fix the triangular unit diagonal case.
351 :    
352 :     * R/Matrix.R: define and
353 :     * NAMESPACE: export as.numeric() and as.logical() methods.
354 :     Let's hope these do not badly slow down something...
355 :     Finally export the zapsmall() method.
356 :    
357 : bates 1388 2006-08-17 Douglas Bates <bates@R-project.org>
358 :    
359 :     * src/dgCMatrix.[ch] (dgCMatrix_matrix_solve), src/init.c,
360 :     R/dgCMatrix.R: solve methods for dgCMatrix and dense RHS.
361 :     * src/dtCMatrix.c :Remove code that is no longer used
362 :     * R/dtCMatrix.R: Use C code for diagU2N in CsparseMatrix classes
363 :    
364 : bates 1370 2006-08-14 Douglas Bates <bates@R-project.org>
365 :    
366 : bates 1373 * src/Csparse.[ch],init.c (Csparse_to_logical): Added utilities
367 :     Csparse_to_logical and Csparse_symmetric_to_general.
368 :     * R/dgCMatrix.R,dsCMatrix.R,Csparse.R : Consolidate general
369 : maechler 1389 coercion methods between CsparseMatrix and TsparseMatrix.
370 : bates 1373
371 :     2006-08-14 Douglas Bates <bates@R-project.org>
372 :    
373 : bates 1370 * R/dtCMatrix.R,dgCMatrix.R,Csparse.R src/init.c,dgCMatrix.[ch],
374 :     Csparse.[ch],chm_common.c,dense.c : Use CHOLMOD code and methods
375 :     for CsparseMatrix, TsparseMatrix, denseMatrix or matrix when
376 :     possible.
377 :    
378 : bates 1368 2006-08-12 Douglas Bates <bates@R-project.org>
379 :    
380 :     * src/chm_common.[ch],Csparse.[ch],Tsparse.[ch],CHMfactor.c,dtTMatrix.c,
381 :     dgTMatrix.c,dgCMatrix.c,dsCMatrix.c,dtTMatrix.c, R/dsTMatrix.R,
382 :     Tsparse.R,Csparse.R,dgTMatrix.R,dsCMatrix.R,lsCMatrix.R:
383 :     generalize conversions between TsparseMatrix, CsparseMatrix,
384 :     denseMatrix and matrix. Preserve triangularity property and
385 :     propagate Dimnames in the easy cases.
386 :    
387 : bates 1365 2006-08-10 Douglas Bates <bates@R-project.org>
388 :    
389 :     * src/lmer.c: adjust checks in glmer_init for S4SXP
390 :     * tests/validObj.R: check of all(eq) should be all(eq@x) - worked
391 :     before S4SXP but for the wrong reasons.
392 :    
393 : bates 1354 2006-08-08 Douglas Bates <bates@R-project.org>
394 :    
395 : bates 1360 * src/Csparse.c (Csparse_crossprod): tcrossprod result has stype = -1.
396 :     Later modified to return the upper triangle only.
397 :     * R/dgTMatrix.R: Remove vestigial crossprod and tcrossprod methods.
398 : maechler 1389
399 : bates 1352 2006-08-07 Douglas Bates <bates@R-project.org>
400 :    
401 :     * src/Csparse.c (Csparse_crossprod): Set stype on result to avoid
402 :     R-level conversion to a sparse symmetric class.
403 :     * R/Tsparse.R,R/Csparse.R (crossprod and tcrossprod methods):
404 :     Remove conversion to sparse symmetric classes (now done in C code).
405 :    
406 : maechler 1349 2006-08-07 Martin Maechler <maechler@stat.math.ethz.ch>
407 :    
408 : maechler 1351 * R/dgCMatrix.R: disable old crossprod and tcrossprod methods
409 :     * man/band.Rd: adapt the \dontshow{} unit test.
410 :    
411 :     2006-08-07 Martin Maechler <maechler@stat.math.ethz.ch>
412 :    
413 : maechler 1349 * DESCRIPTION (Version): 0.995-14 for CRAN
414 :    
415 :     * tests/other-pkgs.R: oops: library(Matrix) outside *if* !
416 :    
417 :     * R/sparseMatrix.R (Tsp2grNEL): fixed Tsparse -> graph coercion
418 :     * tests/other-pkgs.R: more checks, sparseMatrix -> graph
419 :    
420 :     * R/Auxiliaries.R (as_Tsparse, as_Rsparse): new
421 :     * R/Tsparse.R (tril, triu, band): methods
422 : bates 1352 * R/dgRMatrix.R (tril, ...): ditto
423 :     * man/band.Rd: ditto
424 : maechler 1349
425 :     2006-08-04 Martin Maechler <maechler@stat.math.ethz.ch>
426 :    
427 :     * R/Matrix.R (head, tail): directly use utils:::head.matrix
428 :     to be up-to-date automatically.
429 :    
430 : maechler 1346 2006-08-03 Martin Maechler <maechler@stat.math.ethz.ch>
431 :    
432 :     * DESCRIPTION (Version): 0.995-13 to be released to CRAN
433 :    
434 :     * DESCRIPTION (Lazydata): no, instead of 'yes' because it fails for:
435 :     * data/CAex.R, inst/external/CAex_slots.rda: replacing data/CAex.rda
436 :     * data/KNex.R, inst/external/KNex_slots.rda: replacing data/KNex.rda
437 :     such that the S4 objects are always created by the current version
438 :     of R and 'Matrix' class definitions.
439 :    
440 : bates 1342 2006-08-01 Douglas Bates <bates@R-project.org>
441 :    
442 :     * R/lmer.R (LMEoptimize method), tests/lmer.R,
443 : maechler 1346 inst/external/test3comp.rda: Added warnings for convergence on
444 : bates 1342 boundary and test cases.
445 :    
446 :     * src/lmer.c (mer_postVar): Modified to return the variances that
447 :     are marginal to the fixed effects, not conditional on them (which
448 :     is what the bVar slot contents represent).
449 :    
450 : bates 1338 2006-07-31 Douglas Bates <bates@R-project.org>
451 :    
452 :     * NAMESPACE, src/lmer.c, R/lmer.R (hatTrace): Add the hatTrace
453 :     function which calls the C function mer_hat_trace2.
454 : maechler 1346
455 : bates 1342 * man/ranef.Rd: Include description of "postVar" argument and
456 :     producing a caterpillar plot.
457 : bates 1338
458 : maechler 1335 2006-07-31 Martin Maechler <maechler@stat.math.ethz.ch>
459 :    
460 :     * NAMESPACE: change "correlation" to "corMatrix"
461 :     * R/AllClass.R: to avoid clash with S3 class in 'nlme'.
462 : bates 1352 * R/dpoMatrix.R: ditto
463 :     * R/lmer.R: ditto
464 : maechler 1335
465 : bates 1338 2006-07-28 Douglas Bates <bates@R-project.org>
466 :    
467 :     * src/lmer.c (internal_mer_RZXinv): Split the calculation of the
468 :     RZXinv slot's contents into a separate internal function that can
469 :     be used in mer_hat_trace.
470 :    
471 : maechler 1331 2006-07-22 Martin Maechler <maechler@stat.math.ethz.ch>
472 :    
473 :     * R/Matrix.R: Coercions "Matrix" -> (sparse|dense)Matrix
474 :     via new smart
475 :     * R/Auxiliaries.R (as_Csparse, as_dense, .M.shapse): new
476 :     utility functions.
477 :    
478 :    
479 : maechler 1330 2006-07-21 Martin Maechler <maechler@stat.math.ethz.ch>
480 :    
481 : maechler 1331 * R/Csparse.R (tril, triu, band): do return *triangular* classed
482 :     matrices when appropriate; band() even symmetric ones.
483 :     (replCmat): extend to potentially all "CsparseMatrix"
484 :     * R/Tsparse.R (replTmat): extend to all "TsparseMatrix"; hence
485 :     allow subassignment for special sparse matrices.
486 :    
487 :     * R/Auxiliaries.R (as_geClass): factor out the .M.kind() functionality
488 :    
489 : maechler 1330 * src/lmer.c (mer_MCMCsamp, glmer_MCMCsamp): new 'verbose'
490 :     argument; in glmer_*(): print only if(verbose).
491 :    
492 :     speed-optimize a few places by moving REAL(.) out of loops.
493 :    
494 :     * src/lmer.h, src/init.h, R/lmer.R: related to above.
495 :    
496 : maechler 1329 2006-07-20 Martin Maechler <maechler@stat.math.ethz.ch>
497 :    
498 :     * R/Matrix.R("["): disable ("Matrix", i = "logical", j = "missing"),
499 :     since that wrongly triggers also for M[ logi , ]
500 :    
501 :     * R/denseMatrix.R: "[" methods now also work e.g. when indexing
502 :     a symmetric matrix that results in a non-symmetric one.
503 :     * R/Auxiliaries.R (as_geClass): new function used in "[" above.
504 :    
505 :     * R/dMatrix.R: make round(M) work as round(M, 0)
506 :    
507 :     * R/dgTMatrix.R (image): coordinate system and axis now use
508 :     1-based indices, not 0-based ones.
509 :    
510 :     * R/Tsparse.R (.ind.prep for "["): get rid of max(<empty>) warning.
511 :     * tests/indexing.R: test it.
512 :    
513 :     * NAMESPACE: export isSymmetric(); has been a generic in "base" for a while;
514 :     * man/isSymmetric-methods.Rd: and document it.
515 :    
516 :     * R/SparseM-conv.R: added coercion methods for some 'SparseM' matrices.
517 :     * man/SparseM-conv.Rd: docu them
518 :    
519 :     * tests/other-pkgs.R: renamed from tests/graph.R and add example
520 :     for 'SparseM' conversions
521 :    
522 :     2006-07-17 Douglas Bates <Douglas.Bates@R-project.org>
523 :    
524 :     * R/Matrix.R (head): added head() and tail() methods.
525 :    
526 :     2006-07-17 Martin Maechler <maechler@stat.math.ethz.ch>
527 :    
528 :     * DESCRIPTION (Version): 0.995-12 released to CRAN
529 :    
530 : maechler 1319 2006-07-15 Martin Maechler <maechler@stat.math.ethz.ch>
531 :    
532 :     * tests/simple.R: add check for correct dsT -> dgT coercion;
533 :     add check for correct printing of symmetric sparse matrices.
534 :    
535 :     * R/Auxiliaries.R (non0ind): return *all* non-0 entry indices also
536 :     for sparse symmetric matrices.
537 :    
538 :     * src/dsTMatrix.c (dsTMatrix_as_dgTMatrix): do not copy the
539 :     diagonal twice.
540 :    
541 : bates 1316 2006-07-11 Douglas Bates <Douglas.Bates@R-project.org>
542 :    
543 :     * src/dsTMatrix.c (dsTMatrix_as_dgTMatrix): Fix a case of INTEGER
544 : maechler 1319 being applied to the x slot (detected by Brian Ripley).
545 : bates 1316
546 : maechler 1315 2006-07-10 Martin Maechler <maechler@stat.math.ethz.ch>
547 :    
548 :     * src/dgCMatrix.c (dgCMatrix_validate): 'p' slot must have correct length.
549 :    
550 :     * R/Auxiliaries.R (isTriC): fix buglet (we were 1-based!)
551 :    
552 :     2006-07-08 Martin Maechler <maechler@stat.math.ethz.ch>
553 :    
554 :     * src/lgCMatrix.c (lgCMatrix_diag): new function
555 :     * R/lgCMatrix.R (diag): for new method
556 :    
557 :     * R/AllClass.R (TsparseMatrix): do use Tsparse_validate
558 :     ==> construction of illegal "*gTMatrix" via new() should
559 :     now be much less easy:
560 :     * tests/Class+Meth.R: assertError() for some illegal "dgT*"
561 :    
562 :     * R/Matrix.R (Matrix): Matrix(0, nrow,ncol) now "goes sparse"
563 :     directly.
564 :     * man/Matrix.Rd: documents it.
565 :    
566 : bates 1311 2006-07-06 Douglas Bates <bates@R-project.org>
567 :    
568 :     * src/pedigree.c (pedigree_inbreeding): Correction in
569 :     initialization. This function is not currently being used and is
570 :     not fully tested.
571 :    
572 : bates 1312 * NAMESPACE, R/{AllClass.R,lmer.R}, src/{init.c,lmer.c}:
573 :     Introduced the glmer class. Added code for mcmcmsamp on glmer
574 :     objects. Modified validity check on pedigree objects to account
575 :     for nonparallel patterns of missingness of parents.
576 : bates 1311
577 : bates 1313 * man/{lmer-class.Rd,mcmcsamp.Rd}: Update documentation for glmer
578 :     class.
579 : maechler 1315
580 :     2006-07-01 Martin Maechler <maechler@stat.math.ethz.ch>
581 :    
582 :     * R/pMatrix.R: coercion pMatrix -> Tsparse
583 :    
584 : bates 1300 2006-06-12 Douglas Bates <bates@R-project.org>
585 :    
586 : maechler 1319 * DESCRIPTION (Version): 0.995-11 released to CRAN
587 :    
588 : bates 1300 * R/lmer.R (mcmcsamp method): Corrected arrangments of names on
589 :     the output from mcmcsamp.
590 :    
591 : bates 1298 2006-06-10 Douglas Bates <bates@R-project.org>
592 :    
593 : bates 1300 * R/lmer.R (simulestimate): added C code for calculating the trace
594 :     of the hat matrix.
595 : bates 1298
596 : maechler 1295 2006-06-09 Martin Maechler <maechler@stat.math.ethz.ch>
597 :    
598 :     * R/diagMatrix.R (setAs): define coercion methods to sparse matrix
599 :     classes.
600 : maechler 1315 * R/sparseMatrix.R etc: multiplication of diagonal and sparse
601 : maechler 1295
602 : maechler 1290 2006-06-08 Martin Maechler <maechler@stat.math.ethz.ch>
603 :    
604 :     * R/dgTMatrix.R (colSums): etc. All four of
605 :     colSums(), rowSums(), colMeans(), rowMeans() now should work for
606 :     all "Matrices".
607 :    
608 : bates 1288 2006-06-01 Douglas Bates <bates@stat.wisc.edu>
609 :    
610 :     * R/lmer.R (panel.ci): Add a reference line at zero and a
611 :     background grid to the qqmath plot of ranef.lmer.
612 :    
613 : bates 1287 2006-05-30 Douglas Bates <bates@stat.wisc.edu>
614 : bates 1284
615 : bates 1287 * R/lmer.R (expandSlash): Functions (non-exported) to allow nested
616 :     grouping factors to be specified in the formula as (1|foo/bar).
617 :    
618 :     2006-05-27 Douglas Bates <bates@stat.wisc.edu>
619 :    
620 : bates 1284 * R/lmer.R (findbars and others): Change check of is.numeric to
621 :     !is.language to resolve the bug reported by Jacob Wegelin.
622 :    
623 :     * src/pedigree.c (pedigree_inbreeding): Initial implementation of
624 :     code to evaluate inbreeding coefficients without calculating T,
625 :     based on code in Sargolzaei and Iwaisaki's paper.
626 :    
627 : bates 1283 2006-05-27 Douglas Bates <bates@stat.wisc.edu>
628 :    
629 :     * R/{lmer.R,AllGeneric.R}, src/{init.c,lmer.[ch]}: Added local
630 :     generic and mer methods for isNested and denomDF. This denomDF was
631 :     an attempt to emulate that in lme but I don't think that makes
632 :     sense. Use the trace of the hat matrix instead.
633 :    
634 : maechler 1271 2006-05-17 Martin Maechler <maechler@stat.math.ethz.ch>
635 :    
636 :     * R/sparseMatrix.R: Matrix <-> graph methods: can no longer use
637 :     the C code depending on a slot structure that's no longer valid.
638 : bates 1352 * src/dgTMatrix.c: ditto (also: src/init.c src/dgTMatrix.h)
639 : maechler 1271
640 :    
641 : bates 1268 2006-05-17 Douglas Bates <bates@stat.wisc.edu>
642 :    
643 :     * R/{AllGeneric.R,Csparse.R},man/band.Rd,NAMESPACE: changed name
644 :     of lowerTriMatrix generic and methods to tril (also upper to triu)
645 :     and added a general band extractor.
646 :    
647 : bates 1267 2006-05-16 Douglas Bates <bates@stat.wisc.edu>
648 :    
649 :     * R/pedigree.R (pedigree): Replace sire and dam values outside the
650 :     allowable range with NAs. Added a corresponding check in the
651 :     validity check for the pedigree class.
652 :    
653 :     * R/[CT]sparse.R ([t]crossprod): The result of single-argument
654 :     crossprod methods now inherits from symmetricMatrix.
655 :    
656 : bates 1265 2006-05-15 Douglas Bates <bates@stat.wisc.edu>
657 :    
658 :     * R/AllGeneric.R (lowerTriMatrix): Added (but did not export)
659 :     generics lowerTriMatrix and upperTriMatrix along with methods for
660 :     the Csparse virtual class. Also added a C function Csparse_band
661 :     that implements these methods by calling cholmod_band.
662 :    
663 : maechler 1264 2006-05-15 Martin Maechler <maechler@stat.math.ethz.ch>
664 :    
665 :     * R/Tsparse.R ("["): column or row subsetting; @Dimnames[k] got
666 :     erased when it was NULL. This led to invalid subselections!
667 :    
668 : bates 1259 2006-04-25 Douglas Bates <bates@stat.wisc.edu>
669 :    
670 :     * R/dtCMatrix.R: avoid coercion of dtCMatrix object to dgCMatrix
671 :     in method for "t" so as not to lose the unit diagonal property.
672 :    
673 : bates 1257 2006-04-19 Douglas Bates <bates@stat.wisc.edu>
674 :    
675 :     * R/lmer.R, R/AllGeneric.R, NAMESPACE: Remove the postVar generic
676 :     and methods. This is now an option to the ranef method for the
677 :     mer class.
678 :    
679 :     * src/cs_utils.c: Ensure that the nz component is -1 for a
680 :     compressed column-oriented matrix. Minor formatting cleanup.
681 :    
682 :     * man/lmer-class.Rd: Document the qqmath method for ranef.lmer
683 :     objects.
684 :    
685 : maechler 1253 2006-04-19 Martin Maechler <maechler@stat.math.ethz.ch>
686 :    
687 :     * R/Auxiliaries.R (diagU2N): new for the solve() methods in
688 :     * R/dtCMatrix.R: where dgC -> dgT coercion now preserves diag = "U".
689 :    
690 : bates 1251 2006-04-15 Douglas Bates <bates@stat.wisc.edu>
691 :    
692 :     * src/cs.[ch],src/cs_utils.[ch] : Added Tim Davis' CSparse library
693 :     in cs.[ch] and utilities to interface to that code in cs_utils.[ch].
694 :    
695 :     * R/dtCMatrix.R, src/dtCMatrix.[ch] : CSparse-based solve methods
696 :     for the dtCMatrix class.
697 : maechler 1253
698 : bates 1247 2006-04-12 Douglas Bates <bates@stat.wisc.edu>
699 :    
700 :     * R/pedigree.R, R/AllClass.R, NAMESPACE: added a pedigree class
701 :     and methods for it.
702 :    
703 : maechler 1245 2006-04-12 Martin Maechler <maechler@stat.math.ethz.ch>
704 :    
705 :     * R/dgCMatrix.R: add storage.mode(.) <- "double" for "matrix"
706 :     arguments, such that M %*% 1:6 now works
707 :     * Tests/matprod.R: test the above
708 :    
709 : bates 1244 2006-04-03 Douglas Bates <bates@stat.wisc.edu>
710 : bates 1243
711 :     * R/lmer.R (qqmath,ranef.lmer-method): added a qqmath method for
712 :     the ranef.lmer class.
713 :    
714 :     * R/AllClass.R, NAMESPACE, R/lmer.R: Added a postVar generic and
715 :     methods to extract the posterior variances from the bVar slot.
716 :    
717 : maechler 1238 2006-03-30 Martin Maechler <maechler@stat.math.ethz.ch>
718 :    
719 :     * R/dtCMatrix.R: allow coercion from dgC* to triangular (dtC*)
720 :     * R/dsCMatrix.R: and symmetric (dsC*) 'Csparse' matrices.
721 :    
722 :     * R/Tsparse.R: Tsparse* -> Csparse* coercion now works and is tested in
723 :     * tests/simple: (extended)
724 :    
725 :     * R/sparseMatrix.R (isTriangular): now using much improved
726 :     * R/Auxiliaries.R (isTriC): new triangularity check for *CMatrix
727 :    
728 : bates 1236 2006-03-23 Douglas Bates <bates@stat.wisc.edu>
729 :    
730 :     * src/dsyMatrix.c (dsyMatrix_as_dspMatrix): Propagate DimNames
731 :     (problem report from Franklin Parlamis). This should be done
732 : maechler 1238 generally.
733 : bates 1236
734 : bates 1234 2006-03-21 Douglas Bates <bates@stat.wisc.edu>
735 :    
736 :     * R/AllClass.R,lmer.R: Change the name of the lmer.ranef class to
737 :     ranef.lmer (like summary.lmer). Add the coef.lmer class and
738 :     update the plot methods.
739 :    
740 : bates 1232 2006-03-20 Douglas Bates <bates@stat.wisc.edu>
741 :    
742 :     * R/lmer.R (resid and ranef methods): Added methods for the
743 :     "residuals" and "resid" generic but only for linear mixed model
744 :     fits. Changed the ranef method to return a list of data frames so
745 :     that the plot methods now work.
746 :    
747 : bates 1230 2006-03-16 Douglas Bates <bates@bates2>
748 :    
749 :     * src/dpoMatrix.c (dpoMatrix_chol): Require n > 0 in call to
750 :     dpotrf - otherwise the BLAS on Mac OS X complains and quits.
751 :    
752 :     * DESCRIPTION (Date): New release
753 :    
754 : maechler 1228 2006-03-15 Martin Maechler <maechler@stat.math.ethz.ch>
755 :    
756 :     * DESCRIPTION (Version): 0.995-6 -- to be released to CRAN
757 :    
758 :     * data/KNex.rda: replacing 'mm' and 'y' by KNex <- list(mm=mm, y=y)
759 :     * man/KNex.Rd: and other help files
760 :     * tests/*.R: several ones needed adaption
761 : bates 1352 * inst/doc/Comparisons.Rnw: ditto
762 : maechler 1228
763 : maechler 1226 2006-03-11 Martin Maechler <maechler@stat.math.ethz.ch>
764 :    
765 :     * R/dgCMatrix.R (replCmat): "[<-" methods for dgCMatrix
766 :    
767 :     * tests/indexing.R: tests for new [<- methods for sparse matrices.
768 :    
769 :     2006-03-10 Martin Maechler <maechler@stat.math.ethz.ch>
770 :    
771 :     * R/dgTMatrix.R (replTmat): "[<-" methods for dgTMatrix
772 :    
773 :     * R/Tsparse.R (.ind.prep): fix out-of-range indexing
774 :    
775 :     2006-03-08 Martin Maechler <maechler@stat.math.ethz.ch>
776 :    
777 :     * R/dMatrix.R: enable things like M [ M < 10 ]
778 :     * R/dgeMatrix.R: implement it
779 :    
780 : maechler 1222 2006-03-06 Martin Maechler <maechler@stat.math.ethz.ch>
781 :    
782 :     * R/AllClass.R: define "summary.mer" and "*.lmer"
783 :     * R/lmer.R (summary): summary(<mer>) computes & returns the above;
784 :     * R/lmer.R (show): now works with summary()
785 :    
786 :     2006-03-04 Martin Maechler <maechler@stat.math.ethz.ch>
787 :    
788 :     * R/dgCMatrix.R: finally direct "Arith" dgC o dgC
789 :     * R/Auxiliaries.R (WhichintersectInd): and other utilities to
790 :     support the above
791 :    
792 : bates 1213 2006-02-07 Douglas Bates <bates@stat.wisc.edu>
793 :    
794 :     * R/lmer.R (lmer): fix initial values of offset and weights for glm.fit.
795 :     Use glmFit$prior.weights for weights in a glmm.
796 :     Allow an option usePQL = FALSE to skip the PQL steps for the
797 :     Laplace method (and, in time, the AGQ method).
798 :    
799 :     * src/lmer.c (mer_factor): Move downdating and factoring of XtX
800 :     into a separate function internal_mer_Xfactor to be able to call
801 :     it from internal_bhat.
802 :    
803 : maechler 1200 2006-01-23 Martin Maechler <maechler@stat.math.ethz.ch>
804 :    
805 :     * tests/Class+Meth.R (tstMatrixClass): function for much better
806 :     testing; now again of all actual classes.
807 :    
808 :     * src/Mutils.c (MAKE_TRIANGULAR_BODY, MAKE_SYMMETRIC_BODY):
809 :     use macros and define make_d_matrix_* and make_i_matrix_*
810 :     where _i_ is for the ldense routines:
811 :    
812 :     * src/ldense.c (ltrMatrix_as_lgeMatrix): provide functions
813 :     * src/ldense.c (lsyMatrix_as_lgeMatrix):
814 :    
815 :     * R/ldenseMatrix.R: use the above in setAs(*,"lgeMatrix")
816 :    
817 :    
818 : maechler 1174 2006-01-16 Martin Maechler <maechler@stat.math.ethz.ch>
819 :    
820 :     * R/Matrix.R (Matrix): has become much "smarter" now auto-producing
821 :     many different kinds of matrices.
822 :     * R/*.R: quite a few new methods were needed for R CMD check with
823 :     new Matrix(). Very good for users playing around.
824 :    
825 :    
826 : maechler 1165 2006-01-15 Martin Maechler <maechler@stat.math.ethz.ch>
827 :    
828 :     * src/dgeMatrix.c (dMatrix_validate): new
829 :     * src/Mutils.c (dense_nonpacked_validate): new
830 :    
831 :     * src/dtrMatrix.c (dtrMatrix_validate): improved/fixed
832 :    
833 :    
834 :     2006-01-14 Douglas Bates <bates@stat.wisc.edu>
835 :    
836 :     * R/AllClass.R (compMatrix), (generalMatrix): new virtual classes
837 :    
838 : bates 1123 2006-01-07 Douglas Bates <bates@stat.wisc.edu>
839 : bates 1119
840 : maechler 1127 * DESCRIPTION (Version): 0.99-6 released to CRAN
841 :    
842 : bates 1119 * src/dgBCMatrix.c (cscb_trcbsm): Fix due to Peter Dalgaard for
843 :     segfault in cases with multiple non-nested grouping factors.
844 :    
845 : maechler 1109 2006-01-03 Martin Maechler <maechler@stat.math.ethz.ch>
846 :    
847 :     * DESCRIPTION (Version): 0.99-4 to be released to CRAN
848 :     (Depends): also on 'utils'
849 :    
850 :     * R/AllClass.R (diagonalMatrix): new class with "ddi*" and "ldi*"
851 :     * R/diagMatrix.R (Diagonal): constructor and methods for
852 :     diagonal matrices
853 :    
854 :     * R/ltTMatrix.R: new "minimal methods"
855 :    
856 : maechler 1091 2005-12-12 Martin Maechler <maechler@stat.math.ethz.ch>
857 :    
858 :     * R/AllGeneric.R (tcrossprod): 2-argument version; here, and for
859 :     all methods (and help files).
860 :    
861 : maechler 1084 2005-12-09 Martin Maechler <maechler@stat.math.ethz.ch>
862 :    
863 :     * R/Auxiliaries.R (dimNamesCheck): fixed thinko -> bug
864 :     for case (dimn. op no_dimn.)
865 :    
866 :     2005-11-14 Douglas Bates <bates@stat.wisc.edu>
867 :    
868 : maechler 1174 * DESCRIPTION (Version): 0.99-2 released to CRAN
869 : maechler 1084
870 : bates 988 2005-10-21 Douglas Bates <bates@stat.wisc.edu>
871 :    
872 :     * R/lmer.R (simulate method): Fixed a drop=FALSE problem reported
873 :     by Julian Faraway.
874 :    
875 : maechler 976 2005-10-06 Martin Maechler <maechler@stat.math.ethz.ch>
876 :    
877 :     * R/Auxiliaries.R (try_as): new utility
878 :     * R/sparseMatrix.R: use try_as() in coercion to original class
879 :    
880 : maechler 956 2005-09-30 Martin Maechler <maechler@stat.math.ethz.ch>
881 :    
882 :     * src/dgCMatrix.c (double_to_csc): and dgeMatrix_to_csc()
883 :    
884 :     2005-09-29 Martin Maechler <maechler@stat.math.ethz.ch>
885 :    
886 :     * R/Auxiliaries.R (dimNamesCheck): added
887 :    
888 :     * R/Matrix.R (as.array), (as.vector): new
889 :    
890 : maechler 954 2005-09-28 Martin Maechler <maechler@stat.math.ethz.ch>
891 :    
892 :     * R/Matrix.R (Matrix): get logical argument 'sparse' with a smart
893 : maechler 956 default.
894 :     * R/AllClass.R: move 'factors' slot toplevel "Matrix";
895 :     "pMatrix" now contains "sparseMatrix"
896 : maechler 954
897 : maechler 948 2005-09-26 Martin Maechler <maechler@stat.math.ethz.ch>
898 :    
899 :     * tests/Class+Meth.R: new tests; t(t(m)) == m
900 :    
901 :     * src/dtCMatrix.c (tsc_transpose): add forgotten "diag" slot
902 :    
903 :     * src/dsTMatrix.c (dsTMatrix_as_dsCMatrix): bad typo (segfault!)
904 :     * src/dtTMatrix.c (dtTMatrix_as_dtCMatrix): new
905 :    
906 :     * R/dspMatrix.R: typo in "t" method
907 :    
908 : maechler 925 2005-09-18 Douglas Bates <bates@wisc.edu>
909 :    
910 :     * R/AllClass.R (TsparseMatrix), CsparseM* and RsparseM*
911 :     * R/Tsparse.R: instead of R/gTMatrix.R
912 :     * R/Csparse.R: new
913 :     * src/Tsparse.c (Tsparse_to_Csparse): new; -> cholmod_()
914 :     * src/Tsparse.c: new; many trivial methods calling cholmod_()
915 :     * src/Csparse.c (Csparse_to_Tsparse), transpose, (mat|cross)prod:
916 :     via cholmod
917 :    
918 :     2005-09-16 Martin Maechler <maechler@stat.math.ethz.ch>
919 :    
920 :     * R/Auxiliaries.R (non0ind): new function using new C code
921 :     * src/dgCMatrix.c (compressed_non_0_ij): new utility
922 :    
923 : bates 917 2005-09-15 Douglas Bates <bates@localhost.localdomain>
924 :    
925 :     * src/chm_common.h: header file required by all C sources that
926 : maechler 1174 call CHOLMOD functions. It defines a cholmod_common structure
927 : bates 917 called 'c' whose address is passed as the last argument to
928 :     (virtually) every CHOLMOD function.
929 :    
930 :     * src/Pattern.c: Simple example of the use of CHOLMOD.
931 :    
932 :     * src/init.c: initialize and finalize the cholmod_common structure.
933 :    
934 :     * src/Makefile: Added source packages CHOLMOD UMFPACK AMD COLAMD
935 :     LDL and CCOLAMD from the U. of Florida sparse matrix library.
936 :    
937 : maechler 908 2005-09-08 Martin Maechler <maechler@stat.math.ethz.ch>
938 :    
939 :     * inst/test-tools.R: new file collecting the utility functions used
940 :     in ./tests/*.R
941 :    
942 :     * R/ddenseMatrix.R (cbind2): new methods for "numeric" and "matrix"
943 :     * R/Matrix.R (cbind2): methods for NULL and missing
944 :    
945 : maechler 886 2005-08-31 Martin Maechler <maechler@stat.math.ethz.ch>
946 :    
947 :     * R/AllClass.R: new "index" class for "[" and "[<-":
948 :     First cut at "symmetricMatrix" and "triangularMatrix"
949 :     * R/gTMatrix.R (.ind.prep): new function;
950 : maechler 1174 Logical and character indexing now work too.
951 : maechler 886 * R/Matrix.R: cheap "[<-" methods for denseMatrix now work
952 :     * tests/indexing.R: new, including *.Rout.save
953 :     * tests/dgTMatrix.R: new
954 :    
955 : bates 876 2005-08-29 Douglas Bates <bates@wisc.edu>
956 :    
957 :     * src/dgTMatrix.c (graphNEL_as_dgTMatrix): Corrected the position
958 :     indicator pos not being updated. Also enforced upper triangular
959 :     for symmetric case. Need to coerce edges component of elements of
960 :     edge list - grr! (Why don't they define their classes cleanly?)
961 :    
962 : maechler 871 2005-08-26 Martin Maechler <maechler@stat.math.ethz.ch>
963 :    
964 :     * R/Matrix.R: added first "[<-" methods; not yet functional
965 : bates 1352 * R/denseMatrix.R: ditto
966 : maechler 871 * man/Subassign-methods.Rd: new help file for these
967 :    
968 :     2005-08-25 Martin Maechler <maechler@stat.math.ethz.ch>
969 :    
970 :     * DESCRIPTION (Version): 0.98-6
971 :    
972 :     * R/denseMatrix.R: new file for "[" fallback methods for all dense
973 :     matrices.
974 :    
975 : maechler 868 2005-08-19 Martin Maechler <maechler@stat.math.ethz.ch>
976 :    
977 :     * src/lgCMatrix.c (lcsc_to_matrix): new; need for
978 :     as( <logical>, "matrix")
979 :    
980 :     * R/pMatrix.R: coercion to "lgTMatrix"
981 :    
982 :     * R/gTMatrix.R: new virtual class to define "[" methods for.
983 :     * man/gTMatrix-class.Rd:
984 :     * General slight re-organization of where "[" methods are defined.
985 :     more to come.
986 :    
987 : maechler 871 2005-08-18 Douglas Bates <bates@wisc.edu>
988 : maechler 868
989 : maechler 1174 * DESCRIPTION (Version): 0.98-5 released to CRAN
990 : maechler 871
991 :     * src/dgTMatrix.c (graphNEL_as_dgTMatrix): add first graphNEL methods
992 :     * .....
993 :    
994 : bates 863 2005-08-18 Douglas Bates <bates@localhost.localdomain>
995 :    
996 :     * R/lmer.R: Corrected naming scheme in mcmcsamp to work with lmer
997 :     or glmer objects.
998 :    
999 : maechler 860 2005-08-17 Martin Maechler <maechler@stat.math.ethz.ch>
1000 :    
1001 :     * DESCRIPTION (Version): 0.98-4 : upload to CRAN
1002 :    
1003 :     2005-08-16 Douglas Bates <bates@localhost.localdomain>
1004 :    
1005 :     * R/HBMM.R: finish re-writing R-only code.
1006 :    
1007 : bates 854 2005-08-15 Douglas Bates <bates@localhost.localdomain>
1008 :    
1009 :     * man/externalFormats.Rd: move documentation for writeHB and
1010 :     writeMM here.
1011 :    
1012 :     * src/mmio.c: replace inclusion of <malloc.h> by <stdlib.h>
1013 :     (suggested by Paul Roecker).
1014 :    
1015 :     * tests/validObj.R (assertError): Comment out test that is failing
1016 :     after recent changes in r-devel.
1017 :    
1018 : maechler 860
1019 : maechler 848 2005-08-11 Martin Maechler <maechler@stat.math.ethz.ch>
1020 :    
1021 :     * R/AllClass.R: intermediate virtual class "denseMatrix"
1022 :     * man/denseMatrix-class.Rd
1023 :     * NAMESPACE: export it, and also export
1024 :     * man/unused-classes.Rd: "iMatrix", "zMatrix" and "ldenseMatrix"
1025 :    
1026 : bates 846 2005-08-10 Douglas Bates <bates@wisc.edu>
1027 :    
1028 : maechler 848 * DESCRIPTION (Version): 0.98-3 to CRAN
1029 :    
1030 : bates 846 * src/dtrMatrix.c (dtrMatrix_validate): fixed up validation and
1031 :     matrix_solve code (which was really, really wrong).
1032 :    
1033 : bates 835 2005-08-07 Douglas Bates <bates@wisc.edu>
1034 : maechler 834
1035 :     * DESCRIPTION (Version): 0.98-2
1036 :    
1037 :     * R/HBMM.R (readHB), (readMM): read Matrix Market formats
1038 :    
1039 :     * R/lmer.R (abbrvNms): new
1040 :     * R/lmer.R (mcmcsamp): allow transformed parameters
1041 : bates 835 * src/HBMM.c (Matrix_writeMatrixMarket): Added read/write routines
1042 :     for the Harwell-Boeing and the MatrixMarket formats.
1043 : maechler 834
1044 :     2005-08-04 Martin Maechler <maechler@stat.math.ethz.ch>
1045 :    
1046 :     * man/dtrMatrix-class.Rd: add examples
1047 : bates 835 * man/dtpMatrix-class.Rd: ditto; plus note about PROBLEM
1048 : maechler 834
1049 :     * TODO: note the dtpMatrix (docu) bug
1050 :    
1051 :     * R/zzz.R (.onLoad): assignInNamespace("as.matrix", *, "base")
1052 :     in order to ensure that new as.matrix() is used by old functions,
1053 :     e.g., svd(), qr(), eigen(), dist(),..;
1054 :     apply(), also matplot() or pairs().
1055 :    
1056 :    
1057 :     2005-08-03 Martin Maechler <maechler@stat.math.ethz.ch>
1058 :    
1059 :     * R/lmer.R: add 'fixme' comments and move the linear vs glm check;
1060 :     add comments about 'control' / lmerControl() arguments
1061 :    
1062 : bates 835 2005-07-27 Douglas Bates <bates@wisc.edu>
1063 : bates 820
1064 : bates 835 * man/sleepstudy.Rd: Added the sleep data set.
1065 : maechler 1174 * DESCRIPTION (Version): 0.98-1 released to CRAN
1066 : bates 820
1067 : bates 835 2005-07-12 Douglas Bates <bates@wisc.edu>
1068 : maechler 834 * man/sleepstudy.Rd: Added the sleep data set.
1069 :    
1070 : bates 809 * R/lmer.R (glmmMCMC): Added PACKAGE = "Matrix" in a couple of
1071 :     .Call calls that were producing spurious output.
1072 :    
1073 : bates 835 2005-07-05 Douglas Bates <bates@wisc.edu>
1074 : bates 801
1075 :     * R/lmer.R (lmer): stored updated variance component estimates in
1076 :     mer object for the generalized model. (Bug reported by Renaud
1077 :     Lancelot).
1078 :    
1079 : bates 835 2005-07-03 Douglas Bates <bates@wisc.edu>
1080 : bates 794
1081 :     * src/lmer.c (glmer_devAGQ): Added AGQ for single grouping factor,
1082 :     unidimensional case.
1083 :    
1084 : bates 835 2005-06-08 Douglas Bates <bates@wisc.edu>
1085 : maechler 791
1086 :     * DESCRIPTION (Version): 0.96-1
1087 :    
1088 : maechler 1174 * moved lmer-class' R and C code moved from lme4 to here
1089 : maechler 791
1090 : bates 835 2005-06-04 Douglas Bates <bates@wisc.edu>
1091 : bates 763
1092 :     * R/dgCMatrix.R: Call to csc_matrix_mm used undefined arguments
1093 :     (reported by Guissepe Ragusa <gragusa@ucsd.edu>)
1094 :    
1095 : bates 835 2005-06-02 Douglas Bates <bates@wisc.edu>
1096 : bates 763
1097 :     * src/Makefile.win: Forgot to update this when Makefile changed.
1098 :    
1099 : bates 835 2005-05-11 Douglas Bates <bates@wisc.edu>
1100 : bates 726
1101 :     * src/dgCMatrix.c (csc_transpose): Simplified function fixing a
1102 :     bug reported by Kurt Hornik and Michael Hahsler.
1103 :    
1104 : bates 835 2005-05-10 Douglas Bates <bates@wisc.edu>
1105 : bates 725
1106 :     * src/lgCMatrix.c (Matrix_lgClgCmm): Implementation of methods for
1107 :     logical sparse matrices. These will also be used in the symbolic
1108 :     analysis for lmer objects.
1109 :    
1110 :     * src/dsCMatrix.c (dsCMatrix_matrix_solve): Copied the dimensions
1111 :     of b to the result. Fixes bug reported by Jean.Coursol@math.u-psud.fr
1112 : maechler 791
1113 : bates 835 2005-05-06 Douglas Bates <bates@wisc.edu>
1114 : bates 714
1115 :     * src/dgeMatrix.c (dgeMatrix_colsums): Added an implementation of
1116 :     colMeans, colSums, rowMeans and rowSums.
1117 :    
1118 : bates 835 2005-04-18 Douglas Bates <bates@wisc.edu>
1119 : bates 692
1120 :     * src/lgCMatrix.[ch]: code for _validate method and stub for
1121 :     multiplication operation.
1122 :    
1123 :     * src/dgeMatrix.c (dgeMatrix_matrix_solve): Passing wrong argument
1124 :     to dgetrs.
1125 :    
1126 :     * src/init.c: Fix cut-and-paste error in definition of
1127 :     dgeMatrix_matrix_solve
1128 :    
1129 :     * src/{many files}: Tighten code by using ALLOC_SLOT.
1130 :    
1131 : bates 835 2005-04-15 Douglas Bates <bates@wisc.edu>
1132 : bates 692
1133 :     * R/AllClass.R: Add lgTMatrix and lgCMatrix classes
1134 :    
1135 :     * DESCRIPTION: Eliminate import of stats.
1136 :    
1137 : maechler 791
1138 : bates 835 2005-04-06 Douglas Bates <bates@wisc.edu>
1139 : bates 692
1140 :     * R/AllClass.R : add logical sparse matrix classes
1141 :    
1142 : maechler 687 2005-04-01 Martin Maechler <maechler@stat.math.ethz.ch>
1143 :    
1144 :     * R/dgTMatrix.R: add "[" method for triplet matrices
1145 :     * R/sparseMatrix.R: and other sparse ones; --> add show() for sparse
1146 :    
1147 : bates 835 2005-03-31 Douglas Bates <bates@wisc.edu>
1148 : maechler 687
1149 :     * DESCRIPTION (Version): release 0.95-5 to CRAN
1150 :    
1151 :     * R/dMatrix.R: add %*%, crossprod and solve "fallback" methods
1152 :     * R/sparseMatrix.R: %*%, crossprod()
1153 :     * R/dgeMatrix.R: more "fallback" methods for numeric/dense matrices
1154 :     * man/*.Rd: move method definitions to 'Matrix' and 'dMatrix'
1155 :     * src/lmer.c (lmer_fitted): fix thinko
1156 :    
1157 : maechler 676 2005-03-26 Martin Maechler <maechler@stat.math.ethz.ch>
1158 :    
1159 :     * R/AllClass.R: add two virtual sparse classes ``on top''
1160 :    
1161 :     2005-03-24 Martin Maechler <maechler@stat.math.ethz.ch>
1162 :    
1163 :     * R/AllClass.R (setClass): use "VIRTUAL" for the virtual classes;
1164 :     correspondingly fix examples and tests/ since new()
1165 :     doesn't work for virtual classes.
1166 :    
1167 : maechler 658 2005-03-17 Martin Maechler <maechler@stat.math.ethz.ch>
1168 :    
1169 :     * R/Matrix.R (as.matrix): method and one for unname()
1170 :     * tests/dpoMatrix.R: tests should now be less platform dependent;
1171 :     also run for R 2.1.0; using as.matrix()
1172 :    
1173 : bates 835 2005-03-15 Douglas Bates <bates@wisc.edu>
1174 : maechler 658
1175 :     * R/pMatrix.R: "pMatrix" class added
1176 :     * ....
1177 :    
1178 : bates 835 2005-03-14 Douglas Bates <bates@wisc.edu>
1179 : bates 645
1180 :     * R/dtpMatrix.R: Add unpack method and an example.
1181 :    
1182 :     * src/dsyMatrix.c (dsyMatrix_trf): Add BunchKaufman factorization
1183 :     of general symmetric matrices and associated S4 methods.
1184 :    
1185 : maechler 658 2005-03-10 Martin Maechler <maechler@stat.math.ethz.ch>
1186 :     +
1187 :     2005-03-05 Martin Maechler <maechler@stat.math.ethz.ch>
1188 :    
1189 :     * R/dgeMatrix.R (setAs): and many other files: more coercion,
1190 :     crossprod() and "%*%" methods added; tests, too.
1191 :     * tests/matprod.R: new, for testing these
1192 :    
1193 : bates 835 2005-03-03 Douglas Bates <bates@wisc.edu>
1194 : bates 599
1195 :     * src/lmer.c (lmer_fitted): Added.
1196 :    
1197 : bates 835 2005-03-02 Douglas Bates <bates@wisc.edu>
1198 : bates 596
1199 :     * R/dsTMatrix.R: Conversion from dsTMatrix to dsCMatrix
1200 :    
1201 : bates 835 2005-02-28 Douglas Bates <bates@wisc.edu>
1202 : bates 582
1203 :     * src/*.c,po/,inst/po: Internationalization and localization of
1204 :     the package.
1205 :    
1206 :     * src/ldl.[ch]: Removed these as their contents are referenced in the
1207 :     R_ldl.c file.
1208 :    
1209 :     * src/flame.[ch]: Removed these source files.
1210 : maechler 658
1211 : bates 582 * src/dtrMatrix.c (make_array_triangular): Move to Mutils
1212 :    
1213 :     * src/LU.[ch],src/init.c: absorb in factorizations
1214 :    
1215 :     * src/Mutils.h: prepare for internationalization
1216 :    
1217 :     * src/cblas.h: move the enum definitions to Mutils.h and remove
1218 :     this file
1219 :    
1220 : maechler 578 2005-02-26 Martin Maechler <maechler@stat.math.ethz.ch>
1221 :    
1222 : maechler 579 * R/dgeMatrix.R: provide "dimnames" and "dimnames<-" methods
1223 :    
1224 :     * R/dtrMatrix.R: fix t() method
1225 :    
1226 : maechler 578 * R/dgeMatrix.R: define group methods "Arith", "Math", "Math2"
1227 : maechler 658 * NAMESPACE: export them (and import generics from "methods")
1228 : maechler 578 * tests/group-methods.R : and test them.
1229 :    
1230 :     * src/dtrMatrix.c (dtrMatrix_as_dgeMatrix): prevent seg.fault in
1231 :     border case
1232 :    
1233 :     2005-02-24 Douglas Bates <bates@stat.wisc.edu>
1234 :    
1235 : maechler 658 * DESCRIPTION (Version): 0.95-2 released to CRAN
1236 : maechler 578
1237 :     * src/dgBCMatrix.c:
1238 :     * src/lmer.c: many changes
1239 :     * ...
1240 :    
1241 : maechler 512 2005-02-04 Martin Maechler <maechler@stat.math.ethz.ch>
1242 :    
1243 :     * R/Matrix.R: add more sophisticated show() method.
1244 :    
1245 : maechler 578 2005-02-02 Douglas Bates <bates@stat.wisc.edu>
1246 :    
1247 :     * */* : almost complete reorganization of classes.
1248 :    
1249 : bates 835 2005-01-26 Douglas Bates <bates@wisc.edu>
1250 : bates 460
1251 :     * R/AllGeneric.R: Added matrix exponential generic expm and a method
1252 :     for the geMatrix class.
1253 :    
1254 : bates 835 2005-01-24 Douglas Bates <bates@wisc.edu>
1255 : bates 460
1256 :     * src/Makefile (clean): Remove *.a and *.so
1257 :    
1258 :     * man/cscBlocked-class.Rd: Remove reference to the lmer-class.
1259 :    
1260 : bates 835 2005-01-23 Douglas Bates <bates@wisc.edu>
1261 : bates 460
1262 : maechler 658 * src/lmer.c (Lind): Definition of Lind was backwards. This only
1263 : bates 460 had an effect in cases with more than 2 grouping factors.
1264 :    
1265 : bates 835 2005-01-03 Douglas Bates <bates@wisc.edu>
1266 : bates 415
1267 :     * src/lmeRep.c (lmer_variances): change from lmeRep to lmer
1268 :    
1269 : bates 835 2004-12-23 Douglas Bates <bates@wisc.edu>
1270 : bates 410
1271 :     * src/init.c (R_init_Matrix): Reorder calls to R_registerRoutines
1272 :     and R_useDynamicSymbols (suggested by B.D.Ripley).
1273 :    
1274 : bates 835 2004-12-14 Douglas Bates <bates@wisc.edu>
1275 : bates 392
1276 :     * R/sscMatrix.R: Add determinant methods
1277 :    
1278 :     * src/triplet.[ch],src/init.c (triplet_to_matrix): Add a coercion
1279 :     for tripletMatrix to matrix.
1280 :    
1281 : bates 835 2004-12-13 Douglas Bates <bates@wisc.edu>
1282 : bates 388
1283 : bates 392 * R/AllClass.R (.onLoad): Eliminate the bbCrosstab class, which is
1284 :     no longer used.
1285 :    
1286 : bates 388 * src/R_ldl.c: Created an R-specific version of the ldl.[ch] files
1287 :     with dynamic allocation of scratch arrays.
1288 :    
1289 :     * src/ssclme.c (ssclme_copy_ctab): Fixed bug in creation of ZtZ
1290 :     for multivariate random effects with multiple grouping factors.
1291 :     Fixes part but not all of #15.
1292 :    
1293 : bates 835 2004-12-03 Douglas Bates <bates@wisc.edu>
1294 : bates 375
1295 :     * src/lmeRep.c (lmeRep_factor): order of operations for multiple
1296 :     scalar grouping factors corrected.
1297 :    
1298 : bates 835 2004-11-29 Douglas Bates <bates@wisc.edu>
1299 : bates 375
1300 :     * src/bCrosstab.c: remove diag_update which is no longer used
1301 :    
1302 : bates 835 2004-11-16 Douglas Bates <bates@wisc.edu>
1303 : bates 350
1304 :     * src/Metis_utils.c: Move metis.h include to C sources so that the
1305 :     .h file can be included.
1306 :    
1307 : bates 835 2004-11-12 Douglas Bates <bates@wisc.edu>
1308 : bates 342
1309 : bates 350 * src/LU.c,geMatrix.c,trMatrix.c, etc.:
1310 : bates 342 Complete allocation of slots in NEW_OBJECT.
1311 :    
1312 :     * src/Mutils.h: Moved list of symbols to an include file
1313 :    
1314 : bates 835 2004-11-11 Douglas Bates <bates@wisc.edu>
1315 : bates 342
1316 :     * src/geMutils.c (Matrix_init): remove unused function
1317 :    
1318 : bates 835 2004-11-10 Douglas Bates <bates@wisc.edu>
1319 : bates 342
1320 :     * src/cscMatrix.c (csc_to_imagemat): removed unused function
1321 :    
1322 : bates 835 2004-11-05 Douglas Bates <bates@wisc.edu>
1323 : bates 327
1324 :     * src/Makefile.win (SOURCES_C): Keep consistent with Makefile
1325 :    
1326 : bates 835 2004-10-27 Douglas Bates <bates@wisc.edu>
1327 : bates 303
1328 :     * R/pdmatrix.R: remove PACKAGE="Matrix" in .Call calls
1329 :    
1330 : bates 835 2004-10-04 Douglas Bates <bates@wisc.edu>
1331 : bates 296
1332 :     * src/init.c: Created R_init_Matrix and added registration of C
1333 :     routines.
1334 :    
1335 : bates 835 2004-10-02 Douglas Bates <bates@wisc.edu>
1336 : bates 283
1337 :     * R/tripletMatrix.R: Force a require(lattice) for the image methods.
1338 :    
1339 : bates 835 2004-06-15 Douglas Bates <bates@wisc.edu>
1340 : bates 229
1341 :     * man/trMatrix-class.Rd: Escape the % chars in .Rd files.
1342 :    
1343 : bates 111 2004-04-20 Douglas Bates <bates@stat.wisc.edu>
1344 :    
1345 :     * src/Makefile.win ($(SHLIB)): Modifications per Uwe Ligges.
1346 :    
1347 : bates 109 2004-04-19 Douglas Bates <bates@stat.wisc.edu>
1348 :    
1349 :     * src/ssclme.c (ssclme_update_mm): fix logic error in
1350 :     ssclme_update_mm
1351 :    
1352 : bates 105 2004-04-18 Douglas Bates <bates@stat.wisc.edu>
1353 :    
1354 :     * src/ssclme.c (ssclme_coef, ssclme_coefGets): Create consistency
1355 :     in the order of unconstrained and constrained parameters.
1356 :     (ssclme_gradient): Added the gradients (not yet correct for
1357 :     multidimensional, unconstrained case).
1358 :    
1359 : bates 78 2004-04-14 Douglas Bates <bates@stat.wisc.edu>
1360 :    
1361 :     * src/ssclme.c (ssclme_EMsteps): Fix logic in REML update
1362 :    
1363 :     * src/Makefile.win: Remove unneeded ranlib call
1364 :    
1365 : bates 71 2004-04-12 Douglas Bates <bates@stat.wisc.edu>
1366 :    
1367 :     * DESCRIPTION (Version): New release
1368 :    
1369 :     * src/Makefile.win: Update Makefile.win to umfpack removal.
1370 :    
1371 : bates 49 2004-04-05 Douglas Bates <bates@bates2_home>
1372 :    
1373 :     * src/triplet_to_col.c: Create triplet_to_col as a native
1374 : maechler 658 function, not the version from umfpack. There were problems with
1375 : bates 49 the configuration of UMFPACK for 64-bit processors and there was
1376 :     only one umfpack routine being used so I moved it here.
1377 :    
1378 : bates 45 2004-04-04 Douglas Bates <bates@bates2_home>
1379 :    
1380 :     * src/ssclme.c (ssclme_variances): New function.
1381 :    
1382 : bates 28 2004-03-28 Douglas Bates <bates@bates2_home>
1383 :    
1384 :     * src/ssclme.c (ssclme_fitted): Added function.
1385 :    
1386 : bates 22 2004-03-27 Douglas Bates <bates@bates2_home>
1387 :    
1388 :     * src/ssclme.c (ssclme_transfer_dimnames): Add new function to
1389 :     store the dimnames in the XtX and bVar slots
1390 :     (ssclme_update_mm): Change the dimensions of the bVar slot
1391 :     components and the returned value from ssclme_ranef.
1392 :    
1393 : bates 10 2004-03-18 Douglas Bates <bates@stat.wisc.edu>
1394 :    
1395 :     * R/{pdMat.R,pdIdent.R,pdLogChol.R,pdMatrixLog.R,pdNatural.R},
1396 :     src/{pdMat.c,pdIdent.c,pdLogChol.c,pdNatural.c},
1397 :     tests/{pdCompSymm.R,pdDiag.R,pdIdent.R,pdLogChol.R,pdNatural.R},
1398 :     man/{pdMat-class.Rd,pdmatrix-class.Rd,corrmatrix-class.Rd,
1399 :     pdDiag-class.Rd,pdIdent-class.Rd,pdNatural-class.Rd,
1400 :     pdLogChol-class.Rd,coefGets.Rd,pdCompSymm-class.Rd,
1401 :     pdfactor-class.Rd,pdFactor.Rd,pdMatrix.Rd,
1402 :     pdBlocked-class.Rd},AllClass.R,AllGeneric.R:
1403 :     Moved the pdMat classes from the lme4 package.
1404 :    
1405 :     2004-03-02 Douglas Bates <bates@stat.wisc.edu>
1406 :    
1407 :     * man/ssclme-class.Rd: Update definition and documentation of the
1408 :     ssclme class to include the DIsqrt slot.
1409 :    
1410 :     * src/ssclme.c (ssclme_deviance): Modify order of computation
1411 :     (much faster using dsyrk, a level 3 BLAS routine).
1412 :    
1413 :     * src/Makefile (SUBLIBS): Change definition (K. Hornik)
1414 :    
1415 :     2004-02-28 Douglas Bates <bates@stat.wisc.edu>
1416 :    
1417 :     * tests/ssclme.R: Modify the test to account for the permutation
1418 :     of the levels of the grouping factors.
1419 :    
1420 :     2004-02-23 Douglas Bates <bates@stat.wisc.edu>
1421 :    
1422 :     * R/ssclme.R,src/ssclme.c (ssclme): Move slots of sscCrosstab slot
1423 :     directly into the ssclme class definition.
1424 :    
1425 :     2004-02-22 Douglas Bates <bates@stat.wisc.edu>
1426 :    
1427 :     * DESCRIPTION (Date): New release
1428 :    
1429 :     * man/ssclme-class.Rd: new file.
1430 :    
1431 :     * src/ssclme.c (ssclme_loglik): major revisions in design. It
1432 :     works and it's fast!
1433 :    
1434 :     2004-02-17 Douglas Bates <bates@stat.wisc.edu>
1435 :    
1436 :     * src/taucs/Makefile.win (lib): Change "ar" to "$(AR)" (B.Ripley)
1437 :    
1438 :     2004-02-16 Douglas Bates <bates@stat.wisc.edu>
1439 :    
1440 :     * DESCRIPTION (Date): New release
1441 :    
1442 :     * NAMESPACE: Don't export ssclme.
1443 :    
1444 :     * data/ScotsSec.rda, man/ScotsSec.Rd: Add Scottish secondary
1445 :     school data.
1446 :    
1447 :     2004-02-11 Douglas Bates <bates@stat.wisc.edu>
1448 :    
1449 :     * src/sscCrosstab.c (sscCrosstab): Added a row to the incidence to
1450 :     keep track of the fixed-effects and the response. Counts also
1451 :     gets an extra element, which is always one.
1452 :    
1453 :     * src/ldl.c: Include these routines from Tim Davis' LDL package.
1454 :    
1455 :     2004-02-10 Douglas Bates <bates@stat.wisc.edu>
1456 :    
1457 :     * src/cscMatrix.c (csc_transpose): new function
1458 :    
1459 :     * src/Mutils.c (csc_sort_columns): perm/iperm confusion corrected
1460 :     (csc_components_transpose): new function
1461 :    
1462 :     2004-02-06 Douglas Bates <bates@stat.wisc.edu>
1463 :    
1464 :     * src/triplet.c (triplet_validate): Fix Dim slot on generated
1465 :     triplets
1466 :    
1467 :     2004-01-30 Douglas Bates <bates@stat.wisc.edu>
1468 :    
1469 :     * R/sscCrosstab.R (sscCrosstab): Added sscCrosstab generator function.
1470 :    
1471 :     * src/LU.h (MATRIX_LU_H): Add #ifndef #define ... #endif to this
1472 :     and all other .h files in src.
1473 :    
1474 :     * src/Makefile.win: This and other Makefile.win files contributed
1475 :     by Brian Ripley.
1476 :    
1477 :     2004-01-27 Douglas Bates <bates@stat.wisc.edu>
1478 :    
1479 :     * R/syMatrix.R: Added methods for "%*%".
1480 :    
1481 :     * R/Hilbert.R (Hilbert): Changed Hilbert function to return a
1482 :     poMatrix object.
1483 :    
1484 :     2004-01-26 Douglas Bates <bates@stat.wisc.edu>
1485 :    
1486 :     * man/sscChol-class.Rd,man/mm.Rd,man/y.Rd: Added man pages.
1487 :    
1488 :     2004-01-25 Douglas Bates <bates@bates2_home>
1489 :    
1490 :     * inst/doc/Introduction.Rnw,Comparisons.Rnw: Added vignettes.
1491 :    
1492 :     * R/csc.R: Convert all cscMatrix classes to use Dim slot instead
1493 :     of nrow.
1494 :    
1495 :     2003-12-31 Douglas Bates <bates@stat.wisc.edu>
1496 :    
1497 :     * src/taucs/taucs.h: Moved taucs.h, amd.h, and umfpack.h into
1498 :     subdirectories.
1499 :    
1500 :     2003-12-08 Douglas Bates <bates@stat.wisc.edu>
1501 :    
1502 :     * src/taucs.h: Accidently referred to global header files
1503 :     instead of local files.
1504 :    
1505 :     2003-12-04 Douglas Bates <bates@stat.wisc.edu>
1506 :    
1507 :     * R/AllClass.R: Lots of changes. Removed all the lapack++ code
1508 :     and methods and replaced all classes with S4 classes.
1509 :    
1510 :     2003-04-19 Douglas Bates <bates@stat.wisc.edu>
1511 :    
1512 :     * R/det.R,man/det.Rd: Change name of det generic to determinant
1513 :    
1514 :     * src/R_LapackPP.cc: Change method of calculating determinants
1515 :    
1516 :     2003-02-03 Douglas Bates <bates@stat.wisc.edu>
1517 :    
1518 :     * DESCRIPTION (Version): removed empty data directory as requested
1519 :     by CRAN maintainers. Changed version number and date.
1520 :    
1521 :     2002-10-23 Douglas Bates <bates@stat.wisc.edu>
1522 :    
1523 :     * src/laindex.h: Applied patches from Brian Ripley for compilation
1524 :     under Windows.
1525 :    
1526 :     * Added configure.win and src/Makevars.win as requested by Brian
1527 :     Ripley.
1528 :    
1529 :     2002-05-03 Douglas Bates <bates@stat.wisc.edu>
1530 :    
1531 :     * src/lamatrix.h: Removing pre-1.2.0 compatibility code per Kurt
1532 :     Hornik.
1533 :    
1534 :     2002-04-24 Douglas Bates <bates@stat.wisc.edu>
1535 :    
1536 :     * configure.ac: Replaced configure.in with configure.ac
1537 :     contributed by Kurt Hornik.
1538 :    
1539 :     * aclocal.m4 (ac_clean_files): Replaced this with Kurt Hornik's
1540 :     version for R-1.5.0
1541 :    
1542 : maechler 512
1543 : bates 10 2001-12-10 Douglas Bates <bates@stat.wisc.edu>
1544 :    
1545 :     * man/eigen.Rd: Removed the .Alias in the example

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