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Annotation of /pkg/ChangeLog

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

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