SCM

SCM Repository

[matrix] Annotation of /pkg/ChangeLog
ViewVC logotype

Annotation of /pkg/ChangeLog

Parent Directory Parent Directory | Revision Log Revision Log


Revision 1475 - (view) (download)

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

root@r-forge.r-project.org
ViewVC Help
Powered by ViewVC 1.0.0  
Thanks to:
Vienna University of Economics and Business Powered By FusionForge