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Annotation of /pkg/ChangeLog

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Revision 1507 - (view) (download)

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

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