SCM

SCM Repository

[matrix] Annotation of /pkg/ChangeLog
ViewVC logotype

Annotation of /pkg/ChangeLog

Parent Directory Parent Directory | Revision Log Revision Log


Revision 1445 - (view) (download)

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