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Annotation of /pkg/ChangeLog

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

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