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Annotation of /pkg/ChangeLog

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Revision 1646 - (view) (download)

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

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