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Annotation of /pkg/ChangeLog

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Revision 1572 - (view) (download)

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

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