SCM

SCM Repository

[matrix] Annotation of /pkg/ChangeLog
ViewVC logotype

Annotation of /pkg/ChangeLog

Parent Directory Parent Directory | Revision Log Revision Log


Revision 1467 - (view) (download)

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