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Annotation of /pkg/ChangeLog

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Revision 1548 - (view) (download)

1 : maechler 1548 2006-09-11 Martin Maechler <maechler@stat.math.ethz.ch>
2 :    
3 :     * R/AllClass.R ("nMatrix"): and subclasses for "nonzero pattern"
4 :     Matrices, since "lMatrix", also "lsparseM" can have NA
5 :     * R/ndenseMatrix.R, etc: new source files
6 :     * man/nsparseMatrix-classes.Rd, etc: new help files
7 :     * tests/: adaptions
8 :     * src/chm_common.c (chm_dense_to_SEXP): and others:
9 :     new 'Rkind' argument: "l*" and "d*" both use CHOLMOD_REAL
10 :     * src/Csparse.c, etc: dito
11 :    
12 : bates 1546 2006-09-11 Douglas Bates <bates@R-project.org>
13 :    
14 :     * src/Mutils.[ch],init.c inst/include/*.h: Move the
15 :     alloc_d**Matrix functions to the lme4 package.
16 :    
17 : bates 1543 2006-09-09 Douglas Bates <bates@R-project.org>
18 :    
19 :     * src/dsCMatrix.c (dsCMatrix_Cholesky): igoring LDL = FALSE now
20 : maechler 1544 fixed
21 : bates 1543
22 : maechler 1544 2006-09-09 Martin Maechler <maechler@stat.math.ethz.ch>
23 :    
24 : maechler 1548 * R/lMatrix.R: new
25 :    
26 : maechler 1544 * R/sparseMatrix.R (Tsp2grNEL): do not yet use graph::foo()
27 :    
28 :     * R/dgeMatrix.R: do not define tcrossprod() methods for "matrix"
29 :     * man/tcrossprod.Rd: dito
30 :    
31 : bates 1538 2006-09-08 Douglas Bates <bates@stat.wisc.edu>
32 :    
33 :     * inst/include/Matrix_stubs.c,Matrix.h: Add declarations and stubs
34 :     for exported functions
35 :     * src/Makefile, src/CHOLMOD/Lib/Makefile, src/Metis,CAMD,CCOLAMD:
36 :     Remove partitioning algorithms for sparse matrix reordering. The
37 :     copyright on the Metis code was problematic and the methods were
38 :     rarely used.
39 :     * src/triplet_to_col.[ch],MMHB.[ch]: Remove triplet_to_col. Such
40 :     operations are now done entirely in CHOLMOD code.
41 :    
42 : bates 1517 2006-09-06 Douglas Bates <bates@R-project.org>
43 :    
44 :     * src/Mutils.h: Remove functions that are no longer used.
45 :    
46 : bates 1507 2006-09-04 Douglas Bates <bates@R-project.org>
47 :    
48 :     * src/dtCMatrix.c (dtCMatrix_validate): rename functions.
49 :     * src/DEPS.mkf: update
50 :    
51 : maechler 1481 2006-09-02 Martin Maechler <maechler@stat.math.ethz.ch>
52 :    
53 :     * created branches/Matrix-for-R-2.3.x; on trunk: do
54 :     * DESCRIPTION (Version): 0.9975-0
55 :     (Depends): R (>= 2.4.0)
56 :    
57 : bates 1475 2006-09-01 Douglas Bates <bates@R-project.org>
58 :    
59 :     * R/sparseMatrix.R: Added direct method to CsparseMatrix from graphNEL
60 :    
61 : maechler 1472 2006-09-01 Martin Maechler <maechler@stat.math.ethz.ch>
62 :    
63 :     * R/sparseMatrix.R: add coercion from "ANY" to "sparseMatrix"
64 :     * R/denseMatrix.R: add coercion from "ANY" to "denseMatrix"
65 :    
66 :     * R/Matrix.R ([): use nargs() to disambiguate M[i] and M[i,]
67 :    
68 :     2006-08-31 Martin Maechler <maechler@stat.math.ethz.ch>
69 :    
70 :     * R/sparseMatrix.R (Arith): moved Arith group method one-level up
71 :     from "dsparse" to "sparse" and now go via "Csparse" instead of "dgC"
72 :     * R/dsparseMatrix.R: dito
73 :     * R/Csparse.R: dito
74 :    
75 :     2006-08-31 Martin Maechler <maechler@stat.math.ethz.ch>
76 :    
77 :     * R/dMatrix.R (Compare): improve availability of "<", etc
78 :     * R/Auxiliaries.R (asTuniq): new; also make use of R 2.4.x print(*,max)
79 :    
80 : maechler 1467 2006-08-30 Martin Maechler <maechler@stat.math.ethz.ch>
81 :    
82 :     * R/dgCMatrix.R: aargh: "Arith(<dgC>, numeric)" was wrong because
83 :     of a 0-index which was used as 1-index (..hmm)
84 :    
85 :     * R/sparseMatrix.R (prSpMatrix): fix printing an all-0 sparse Matrix
86 :    
87 :     * R/Auxiliaries.R (all0, is0): for 0-testing in presence of NA's
88 :     * R/Auxiliaries.R (isTriMat): use all0() for 0-testing.
89 :     (.is.diagonal): dito
90 :    
91 :     * R/lgTMatrix.R: as("matrix", "lgTMatrix"): warn about NA's
92 :    
93 :     * R/Matrix.R (Matrix): also work for NA data
94 :    
95 : maechler 1455 2006-08-28 Martin Maechler <maechler@stat.math.ethz.ch>
96 :    
97 :     * R/Matrix.R (Matrix): + 'forceCheck' argument; dimnames setting
98 :     in all cases.
99 :    
100 : bates 1453 2006-08-27 Douglas Bates <bates@R-project.org>
101 :    
102 :     * src/dense.[ch],init.c, R/ddenseMatrix.R, man/band.Rd
103 :     (ddense_band): Added triu, tril and band for ddenseMatrix objects.
104 :    
105 : maechler 1447 2006-08-25 Martin Maechler <maechler@stat.math.ethz.ch>
106 :    
107 :     * src/Mutils.c (dup_mMatrix_as_dgeMatrix): added all subclasses of
108 :     subclasses of "ddenseMatrix"
109 :     * src/init.c et al: outcomment dtrM*_as_dge* and dsyM*_as_dge*_
110 :     * R/ddenseMatrix.R et al: setAs("ddenseMatrix", "dgeMatrix", ..)
111 :     instead of half dozen specialized ones.
112 :    
113 : bates 1445 2006-08-25 Douglas Bates <bates@R-project.org>
114 :    
115 :     * R/lmer.R (qqmath method): Bug fix provided by Emmanuel Tillard
116 :     <tillard@cirad.fr> - ordering standard errors to match effects.
117 :    
118 : bates 1439 2006-08-24 Douglas Bates <bates@R-project.org>
119 : bates 1431
120 : bates 1439 * src/lsCMatrix.c (lsCMatrix_trans): Remove lsCMatrix_chol based
121 :     on R_ldl.
122 :     * R/lCholCMatrix.R,
123 :     src/[dl]CholCMatrix.[ch],R_ldl.[ch],Metis_utils.[ch]: removed
124 :     * src/dsCMatrix.c (dsCMatrix_to_dgTMatrix): use CHOLMOD
125 :     * many files in ./R and ./src: Use more general version of
126 :     dup_mMatrix_as_dgeMatrix to simplify method definitions.
127 : bates 1442 * src/Mutils.c (dup_mMatrix_as_dgeMatrix): Add ddiMatrix,
128 :     dtpMatrix, dspMatrix and dppMatrix conversions.
129 :    
130 : maechler 1447
131 : bates 1439 2006-08-23 Douglas Bates <bates@R-project.org>
132 :    
133 :     * R/AllClass.R,lCholCMatrix.R,src/SOURCES_C.mkf,init.c,NAMESPACE:
134 :     Remove classes lCholCMatrix and dCholCMatrix based on R_ldl code.
135 : bates 1431 * src/dgeMatrix.c: Ensure 'factors' slot exists in result of
136 :     dgeMatrix_crossprod (may need to do this in other places).
137 :     * R/AllGeneric.R,dsCMatrix.R, src/dscMatrix.[ch]: Add Cholesky
138 :     generic and method for dsCMatrix. Use CHOLMOD for chol().
139 :    
140 : bates 1414 2006-08-22 Douglas Bates <bates@R-project.org>
141 :    
142 :     * src/Mutils.c (dup_mMatrix_as_dgeMatrix): updated for general
143 :     types of classed Matrices, matrices or numeric or logical vectors.
144 : bates 1423 * src/init.c: register dup_mMatrix_as_dgeMatrix for coercions.
145 :     * src/chm_common.c,Mutils.h (as_cholmod_factor): Move check_class
146 :     to Mutils.h (as an inline) and change name to Matrix_check_class;
147 :     fixes in as_cholmod_factor and chm_factor_to_SEXP.
148 :     * src/dsCMatrix.[ch]: Use CHOLMOD for dsCMatrix_chol and
149 :     dsCMatrix_matrix_solve. Comment out vestigial functions.
150 :     * src/Csparse.c: use diag_P and uplo_P macros.
151 : maechler 1447
152 : bates 1405 2006-08-21 Douglas Bates <bates@R-project.org>
153 :    
154 :     * src/lmer.c (internal_mer_RZXinv): Fix memory leak caught by
155 : maechler 1447 valgrind.
156 : bates 1411 * tests/matprod.R: Add tests to verify that 'solve' and '%*%' are
157 :     inverses.
158 :     * src/sparseQR.c (sparseQR_validate): add new validation test, fix
159 :     -Wall warnings.
160 :     * src/dppMatrix.c,dtrMatrix.c,dgCMatrix.c,dgeMatrix.c,dspMatrix.c:
161 :     Use dup_mMatrix_as_dgeMatrix.
162 : maechler 1447
163 : bates 1403 2006-08-20 Douglas Bates <bates@R-project.org>
164 :    
165 :     * src/sparseQR.c: Fix thinko in sparseQR_resid_fitted.
166 :     * tests/sparseQR.R: Added
167 :     * man/sparseQR-class.Rd: Document methods for qr.* generics
168 :     * R/sparseQR.R: Return correct # of coefs; fix cut-and-paste errors
169 :    
170 : bates 1398 2006-08-19 Douglas Bates <bates@R-project.org>
171 :    
172 :     * NAMESPACE, R/sparseQR.R, src/init.c,sparseQR.[ch],SOURCES_C.mkf:
173 :     Added methods for sparseQR for qr.qy, qr.qty, qr.coef, qr.resid
174 :     and qr.fitted.
175 :     * src/Mutils.[ch]: Added dup_mMatrix_as_dgeMatrix utility
176 :     * src/dgCMatrix.c: Check for ordering before storing q in dgCMatrix_QR
177 :    
178 : maechler 1389 2006-08-18 Martin Maechler <maechler@stat.math.ethz.ch>
179 :    
180 :     * R/AllGeneric.R: add "qr" and "chol" generics; via 'trick' since
181 :     the base version has no "..." argument.
182 :    
183 :     * R/sparseMatrix.R (prSpMatrix): fix the triangular unit diagonal case.
184 :    
185 :     * R/Matrix.R: define and
186 :     * NAMESPACE: export as.numeric() and as.logical() methods.
187 :     Let's hope these do not badly slow down something...
188 :     Finally export the zapsmall() method.
189 :    
190 : bates 1388 2006-08-17 Douglas Bates <bates@R-project.org>
191 :    
192 :     * src/dgCMatrix.[ch] (dgCMatrix_matrix_solve), src/init.c,
193 :     R/dgCMatrix.R: solve methods for dgCMatrix and dense RHS.
194 :     * src/dtCMatrix.c :Remove code that is no longer used
195 :     * R/dtCMatrix.R: Use C code for diagU2N in CsparseMatrix classes
196 :    
197 : bates 1370 2006-08-14 Douglas Bates <bates@R-project.org>
198 :    
199 : bates 1373 * src/Csparse.[ch],init.c (Csparse_to_logical): Added utilities
200 :     Csparse_to_logical and Csparse_symmetric_to_general.
201 :     * R/dgCMatrix.R,dsCMatrix.R,Csparse.R : Consolidate general
202 : maechler 1389 coercion methods between CsparseMatrix and TsparseMatrix.
203 : bates 1373
204 :     2006-08-14 Douglas Bates <bates@R-project.org>
205 :    
206 : bates 1370 * R/dtCMatrix.R,dgCMatrix.R,Csparse.R src/init.c,dgCMatrix.[ch],
207 :     Csparse.[ch],chm_common.c,dense.c : Use CHOLMOD code and methods
208 :     for CsparseMatrix, TsparseMatrix, denseMatrix or matrix when
209 :     possible.
210 :    
211 : bates 1368 2006-08-12 Douglas Bates <bates@R-project.org>
212 :    
213 :     * src/chm_common.[ch],Csparse.[ch],Tsparse.[ch],CHMfactor.c,dtTMatrix.c,
214 :     dgTMatrix.c,dgCMatrix.c,dsCMatrix.c,dtTMatrix.c, R/dsTMatrix.R,
215 :     Tsparse.R,Csparse.R,dgTMatrix.R,dsCMatrix.R,lsCMatrix.R:
216 :     generalize conversions between TsparseMatrix, CsparseMatrix,
217 :     denseMatrix and matrix. Preserve triangularity property and
218 :     propagate Dimnames in the easy cases.
219 :    
220 : bates 1365 2006-08-10 Douglas Bates <bates@R-project.org>
221 :    
222 :     * src/lmer.c: adjust checks in glmer_init for S4SXP
223 :     * tests/validObj.R: check of all(eq) should be all(eq@x) - worked
224 :     before S4SXP but for the wrong reasons.
225 :    
226 : bates 1354 2006-08-08 Douglas Bates <bates@R-project.org>
227 :    
228 : bates 1360 * src/Csparse.c (Csparse_crossprod): tcrossprod result has stype = -1.
229 :     Later modified to return the upper triangle only.
230 :     * R/dgTMatrix.R: Remove vestigial crossprod and tcrossprod methods.
231 : maechler 1389
232 : bates 1352 2006-08-07 Douglas Bates <bates@R-project.org>
233 :    
234 :     * src/Csparse.c (Csparse_crossprod): Set stype on result to avoid
235 :     R-level conversion to a sparse symmetric class.
236 :     * R/Tsparse.R,R/Csparse.R (crossprod and tcrossprod methods):
237 :     Remove conversion to sparse symmetric classes (now done in C code).
238 :    
239 : maechler 1349 2006-08-07 Martin Maechler <maechler@stat.math.ethz.ch>
240 :    
241 : maechler 1351 * R/dgCMatrix.R: disable old crossprod and tcrossprod methods
242 :     * man/band.Rd: adapt the \dontshow{} unit test.
243 :    
244 :     2006-08-07 Martin Maechler <maechler@stat.math.ethz.ch>
245 :    
246 : maechler 1349 * DESCRIPTION (Version): 0.995-14 for CRAN
247 :    
248 :     * tests/other-pkgs.R: oops: library(Matrix) outside *if* !
249 :    
250 :     * R/sparseMatrix.R (Tsp2grNEL): fixed Tsparse -> graph coercion
251 :     * tests/other-pkgs.R: more checks, sparseMatrix -> graph
252 :    
253 :     * R/Auxiliaries.R (as_Tsparse, as_Rsparse): new
254 :     * R/Tsparse.R (tril, triu, band): methods
255 : bates 1352 * R/dgRMatrix.R (tril, ...): ditto
256 :     * man/band.Rd: ditto
257 : maechler 1349
258 :     2006-08-04 Martin Maechler <maechler@stat.math.ethz.ch>
259 :    
260 :     * R/Matrix.R (head, tail): directly use utils:::head.matrix
261 :     to be up-to-date automatically.
262 :    
263 : maechler 1346 2006-08-03 Martin Maechler <maechler@stat.math.ethz.ch>
264 :    
265 :     * DESCRIPTION (Version): 0.995-13 to be released to CRAN
266 :    
267 :     * DESCRIPTION (Lazydata): no, instead of 'yes' because it fails for:
268 :     * data/CAex.R, inst/external/CAex_slots.rda: replacing data/CAex.rda
269 :     * data/KNex.R, inst/external/KNex_slots.rda: replacing data/KNex.rda
270 :     such that the S4 objects are always created by the current version
271 :     of R and 'Matrix' class definitions.
272 :    
273 : bates 1342 2006-08-01 Douglas Bates <bates@R-project.org>
274 :    
275 :     * R/lmer.R (LMEoptimize method), tests/lmer.R,
276 : maechler 1346 inst/external/test3comp.rda: Added warnings for convergence on
277 : bates 1342 boundary and test cases.
278 :    
279 :     * src/lmer.c (mer_postVar): Modified to return the variances that
280 :     are marginal to the fixed effects, not conditional on them (which
281 :     is what the bVar slot contents represent).
282 :    
283 : bates 1338 2006-07-31 Douglas Bates <bates@R-project.org>
284 :    
285 :     * NAMESPACE, src/lmer.c, R/lmer.R (hatTrace): Add the hatTrace
286 :     function which calls the C function mer_hat_trace2.
287 : maechler 1346
288 : bates 1342 * man/ranef.Rd: Include description of "postVar" argument and
289 :     producing a caterpillar plot.
290 : bates 1338
291 : maechler 1335 2006-07-31 Martin Maechler <maechler@stat.math.ethz.ch>
292 :    
293 :     * NAMESPACE: change "correlation" to "corMatrix"
294 :     * R/AllClass.R: to avoid clash with S3 class in 'nlme'.
295 : bates 1352 * R/dpoMatrix.R: ditto
296 :     * R/lmer.R: ditto
297 : maechler 1335
298 : bates 1338 2006-07-28 Douglas Bates <bates@R-project.org>
299 :    
300 :     * src/lmer.c (internal_mer_RZXinv): Split the calculation of the
301 :     RZXinv slot's contents into a separate internal function that can
302 :     be used in mer_hat_trace.
303 :    
304 : maechler 1331 2006-07-22 Martin Maechler <maechler@stat.math.ethz.ch>
305 :    
306 :     * R/Matrix.R: Coercions "Matrix" -> (sparse|dense)Matrix
307 :     via new smart
308 :     * R/Auxiliaries.R (as_Csparse, as_dense, .M.shapse): new
309 :     utility functions.
310 :    
311 :    
312 : maechler 1330 2006-07-21 Martin Maechler <maechler@stat.math.ethz.ch>
313 :    
314 : maechler 1331 * R/Csparse.R (tril, triu, band): do return *triangular* classed
315 :     matrices when appropriate; band() even symmetric ones.
316 :     (replCmat): extend to potentially all "CsparseMatrix"
317 :     * R/Tsparse.R (replTmat): extend to all "TsparseMatrix"; hence
318 :     allow subassignment for special sparse matrices.
319 :    
320 :     * R/Auxiliaries.R (as_geClass): factor out the .M.kind() functionality
321 :    
322 : maechler 1330 * src/lmer.c (mer_MCMCsamp, glmer_MCMCsamp): new 'verbose'
323 :     argument; in glmer_*(): print only if(verbose).
324 :    
325 :     speed-optimize a few places by moving REAL(.) out of loops.
326 :    
327 :     * src/lmer.h, src/init.h, R/lmer.R: related to above.
328 :    
329 : maechler 1329 2006-07-20 Martin Maechler <maechler@stat.math.ethz.ch>
330 :    
331 :     * R/Matrix.R("["): disable ("Matrix", i = "logical", j = "missing"),
332 :     since that wrongly triggers also for M[ logi , ]
333 :    
334 :     * R/denseMatrix.R: "[" methods now also work e.g. when indexing
335 :     a symmetric matrix that results in a non-symmetric one.
336 :     * R/Auxiliaries.R (as_geClass): new function used in "[" above.
337 :    
338 :     * R/dMatrix.R: make round(M) work as round(M, 0)
339 :    
340 :     * R/dgTMatrix.R (image): coordinate system and axis now use
341 :     1-based indices, not 0-based ones.
342 :    
343 :     * R/Tsparse.R (.ind.prep for "["): get rid of max(<empty>) warning.
344 :     * tests/indexing.R: test it.
345 :    
346 :     * NAMESPACE: export isSymmetric(); has been a generic in "base" for a while;
347 :     * man/isSymmetric-methods.Rd: and document it.
348 :    
349 :     * R/SparseM-conv.R: added coercion methods for some 'SparseM' matrices.
350 :     * man/SparseM-conv.Rd: docu them
351 :    
352 :     * tests/other-pkgs.R: renamed from tests/graph.R and add example
353 :     for 'SparseM' conversions
354 :    
355 :     2006-07-17 Douglas Bates <Douglas.Bates@R-project.org>
356 :    
357 :     * R/Matrix.R (head): added head() and tail() methods.
358 :    
359 :     2006-07-17 Martin Maechler <maechler@stat.math.ethz.ch>
360 :    
361 :     * DESCRIPTION (Version): 0.995-12 released to CRAN
362 :    
363 : maechler 1319 2006-07-15 Martin Maechler <maechler@stat.math.ethz.ch>
364 :    
365 :     * tests/simple.R: add check for correct dsT -> dgT coercion;
366 :     add check for correct printing of symmetric sparse matrices.
367 :    
368 :     * R/Auxiliaries.R (non0ind): return *all* non-0 entry indices also
369 :     for sparse symmetric matrices.
370 :    
371 :     * src/dsTMatrix.c (dsTMatrix_as_dgTMatrix): do not copy the
372 :     diagonal twice.
373 :    
374 : bates 1316 2006-07-11 Douglas Bates <Douglas.Bates@R-project.org>
375 :    
376 :     * src/dsTMatrix.c (dsTMatrix_as_dgTMatrix): Fix a case of INTEGER
377 : maechler 1319 being applied to the x slot (detected by Brian Ripley).
378 : bates 1316
379 : maechler 1315 2006-07-10 Martin Maechler <maechler@stat.math.ethz.ch>
380 :    
381 :     * src/dgCMatrix.c (dgCMatrix_validate): 'p' slot must have correct length.
382 :    
383 :     * R/Auxiliaries.R (isTriC): fix buglet (we were 1-based!)
384 :    
385 :     2006-07-08 Martin Maechler <maechler@stat.math.ethz.ch>
386 :    
387 :     * src/lgCMatrix.c (lgCMatrix_diag): new function
388 :     * R/lgCMatrix.R (diag): for new method
389 :    
390 :     * R/AllClass.R (TsparseMatrix): do use Tsparse_validate
391 :     ==> construction of illegal "*gTMatrix" via new() should
392 :     now be much less easy:
393 :     * tests/Class+Meth.R: assertError() for some illegal "dgT*"
394 :    
395 :     * R/Matrix.R (Matrix): Matrix(0, nrow,ncol) now "goes sparse"
396 :     directly.
397 :     * man/Matrix.Rd: documents it.
398 :    
399 : bates 1311 2006-07-06 Douglas Bates <bates@R-project.org>
400 :    
401 :     * src/pedigree.c (pedigree_inbreeding): Correction in
402 :     initialization. This function is not currently being used and is
403 :     not fully tested.
404 :    
405 : bates 1312 * NAMESPACE, R/{AllClass.R,lmer.R}, src/{init.c,lmer.c}:
406 :     Introduced the glmer class. Added code for mcmcmsamp on glmer
407 :     objects. Modified validity check on pedigree objects to account
408 :     for nonparallel patterns of missingness of parents.
409 : bates 1311
410 : bates 1313 * man/{lmer-class.Rd,mcmcsamp.Rd}: Update documentation for glmer
411 :     class.
412 : maechler 1315
413 :     2006-07-01 Martin Maechler <maechler@stat.math.ethz.ch>
414 :    
415 :     * R/pMatrix.R: coercion pMatrix -> Tsparse
416 :    
417 : bates 1300 2006-06-12 Douglas Bates <bates@R-project.org>
418 :    
419 : maechler 1319 * DESCRIPTION (Version): 0.995-11 released to CRAN
420 :    
421 : bates 1300 * R/lmer.R (mcmcsamp method): Corrected arrangments of names on
422 :     the output from mcmcsamp.
423 :    
424 : bates 1298 2006-06-10 Douglas Bates <bates@R-project.org>
425 :    
426 : bates 1300 * R/lmer.R (simulestimate): added C code for calculating the trace
427 :     of the hat matrix.
428 : bates 1298
429 : maechler 1295 2006-06-09 Martin Maechler <maechler@stat.math.ethz.ch>
430 :    
431 :     * R/diagMatrix.R (setAs): define coercion methods to sparse matrix
432 :     classes.
433 : maechler 1315 * R/sparseMatrix.R etc: multiplication of diagonal and sparse
434 : maechler 1295
435 : maechler 1290 2006-06-08 Martin Maechler <maechler@stat.math.ethz.ch>
436 :    
437 :     * R/dgTMatrix.R (colSums): etc. All four of
438 :     colSums(), rowSums(), colMeans(), rowMeans() now should work for
439 :     all "Matrices".
440 :    
441 : bates 1288 2006-06-01 Douglas Bates <bates@stat.wisc.edu>
442 :    
443 :     * R/lmer.R (panel.ci): Add a reference line at zero and a
444 :     background grid to the qqmath plot of ranef.lmer.
445 :    
446 : bates 1287 2006-05-30 Douglas Bates <bates@stat.wisc.edu>
447 : bates 1284
448 : bates 1287 * R/lmer.R (expandSlash): Functions (non-exported) to allow nested
449 :     grouping factors to be specified in the formula as (1|foo/bar).
450 :    
451 :     2006-05-27 Douglas Bates <bates@stat.wisc.edu>
452 :    
453 : bates 1284 * R/lmer.R (findbars and others): Change check of is.numeric to
454 :     !is.language to resolve the bug reported by Jacob Wegelin.
455 :    
456 :     * src/pedigree.c (pedigree_inbreeding): Initial implementation of
457 :     code to evaluate inbreeding coefficients without calculating T,
458 :     based on code in Sargolzaei and Iwaisaki's paper.
459 :    
460 : bates 1283 2006-05-27 Douglas Bates <bates@stat.wisc.edu>
461 :    
462 :     * R/{lmer.R,AllGeneric.R}, src/{init.c,lmer.[ch]}: Added local
463 :     generic and mer methods for isNested and denomDF. This denomDF was
464 :     an attempt to emulate that in lme but I don't think that makes
465 :     sense. Use the trace of the hat matrix instead.
466 :    
467 : maechler 1271 2006-05-17 Martin Maechler <maechler@stat.math.ethz.ch>
468 :    
469 :     * R/sparseMatrix.R: Matrix <-> graph methods: can no longer use
470 :     the C code depending on a slot structure that's no longer valid.
471 : bates 1352 * src/dgTMatrix.c: ditto (also: src/init.c src/dgTMatrix.h)
472 : maechler 1271
473 :    
474 : bates 1268 2006-05-17 Douglas Bates <bates@stat.wisc.edu>
475 :    
476 :     * R/{AllGeneric.R,Csparse.R},man/band.Rd,NAMESPACE: changed name
477 :     of lowerTriMatrix generic and methods to tril (also upper to triu)
478 :     and added a general band extractor.
479 :    
480 : bates 1267 2006-05-16 Douglas Bates <bates@stat.wisc.edu>
481 :    
482 :     * R/pedigree.R (pedigree): Replace sire and dam values outside the
483 :     allowable range with NAs. Added a corresponding check in the
484 :     validity check for the pedigree class.
485 :    
486 :     * R/[CT]sparse.R ([t]crossprod): The result of single-argument
487 :     crossprod methods now inherits from symmetricMatrix.
488 :    
489 : bates 1265 2006-05-15 Douglas Bates <bates@stat.wisc.edu>
490 :    
491 :     * R/AllGeneric.R (lowerTriMatrix): Added (but did not export)
492 :     generics lowerTriMatrix and upperTriMatrix along with methods for
493 :     the Csparse virtual class. Also added a C function Csparse_band
494 :     that implements these methods by calling cholmod_band.
495 :    
496 : maechler 1264 2006-05-15 Martin Maechler <maechler@stat.math.ethz.ch>
497 :    
498 :     * R/Tsparse.R ("["): column or row subsetting; @Dimnames[k] got
499 :     erased when it was NULL. This led to invalid subselections!
500 :    
501 : bates 1259 2006-04-25 Douglas Bates <bates@stat.wisc.edu>
502 :    
503 :     * R/dtCMatrix.R: avoid coercion of dtCMatrix object to dgCMatrix
504 :     in method for "t" so as not to lose the unit diagonal property.
505 :    
506 : bates 1257 2006-04-19 Douglas Bates <bates@stat.wisc.edu>
507 :    
508 :     * R/lmer.R, R/AllGeneric.R, NAMESPACE: Remove the postVar generic
509 :     and methods. This is now an option to the ranef method for the
510 :     mer class.
511 :    
512 :     * src/cs_utils.c: Ensure that the nz component is -1 for a
513 :     compressed column-oriented matrix. Minor formatting cleanup.
514 :    
515 :     * man/lmer-class.Rd: Document the qqmath method for ranef.lmer
516 :     objects.
517 :    
518 : maechler 1253 2006-04-19 Martin Maechler <maechler@stat.math.ethz.ch>
519 :    
520 :     * R/Auxiliaries.R (diagU2N): new for the solve() methods in
521 :     * R/dtCMatrix.R: where dgC -> dgT coercion now preserves diag = "U".
522 :    
523 : bates 1251 2006-04-15 Douglas Bates <bates@stat.wisc.edu>
524 :    
525 :     * src/cs.[ch],src/cs_utils.[ch] : Added Tim Davis' CSparse library
526 :     in cs.[ch] and utilities to interface to that code in cs_utils.[ch].
527 :    
528 :     * R/dtCMatrix.R, src/dtCMatrix.[ch] : CSparse-based solve methods
529 :     for the dtCMatrix class.
530 : maechler 1253
531 : bates 1247 2006-04-12 Douglas Bates <bates@stat.wisc.edu>
532 :    
533 :     * R/pedigree.R, R/AllClass.R, NAMESPACE: added a pedigree class
534 :     and methods for it.
535 :    
536 : maechler 1245 2006-04-12 Martin Maechler <maechler@stat.math.ethz.ch>
537 :    
538 :     * R/dgCMatrix.R: add storage.mode(.) <- "double" for "matrix"
539 :     arguments, such that M %*% 1:6 now works
540 :     * Tests/matprod.R: test the above
541 :    
542 : bates 1244 2006-04-03 Douglas Bates <bates@stat.wisc.edu>
543 : bates 1243
544 :     * R/lmer.R (qqmath,ranef.lmer-method): added a qqmath method for
545 :     the ranef.lmer class.
546 :    
547 :     * R/AllClass.R, NAMESPACE, R/lmer.R: Added a postVar generic and
548 :     methods to extract the posterior variances from the bVar slot.
549 :    
550 : maechler 1238 2006-03-30 Martin Maechler <maechler@stat.math.ethz.ch>
551 :    
552 :     * R/dtCMatrix.R: allow coercion from dgC* to triangular (dtC*)
553 :     * R/dsCMatrix.R: and symmetric (dsC*) 'Csparse' matrices.
554 :    
555 :     * R/Tsparse.R: Tsparse* -> Csparse* coercion now works and is tested in
556 :     * tests/simple: (extended)
557 :    
558 :     * R/sparseMatrix.R (isTriangular): now using much improved
559 :     * R/Auxiliaries.R (isTriC): new triangularity check for *CMatrix
560 :    
561 : bates 1236 2006-03-23 Douglas Bates <bates@stat.wisc.edu>
562 :    
563 :     * src/dsyMatrix.c (dsyMatrix_as_dspMatrix): Propagate DimNames
564 :     (problem report from Franklin Parlamis). This should be done
565 : maechler 1238 generally.
566 : bates 1236
567 : bates 1234 2006-03-21 Douglas Bates <bates@stat.wisc.edu>
568 :    
569 :     * R/AllClass.R,lmer.R: Change the name of the lmer.ranef class to
570 :     ranef.lmer (like summary.lmer). Add the coef.lmer class and
571 :     update the plot methods.
572 :    
573 : bates 1232 2006-03-20 Douglas Bates <bates@stat.wisc.edu>
574 :    
575 :     * R/lmer.R (resid and ranef methods): Added methods for the
576 :     "residuals" and "resid" generic but only for linear mixed model
577 :     fits. Changed the ranef method to return a list of data frames so
578 :     that the plot methods now work.
579 :    
580 : bates 1230 2006-03-16 Douglas Bates <bates@bates2>
581 :    
582 :     * src/dpoMatrix.c (dpoMatrix_chol): Require n > 0 in call to
583 :     dpotrf - otherwise the BLAS on Mac OS X complains and quits.
584 :    
585 :     * DESCRIPTION (Date): New release
586 :    
587 : maechler 1228 2006-03-15 Martin Maechler <maechler@stat.math.ethz.ch>
588 :    
589 :     * DESCRIPTION (Version): 0.995-6 -- to be released to CRAN
590 :    
591 :     * data/KNex.rda: replacing 'mm' and 'y' by KNex <- list(mm=mm, y=y)
592 :     * man/KNex.Rd: and other help files
593 :     * tests/*.R: several ones needed adaption
594 : bates 1352 * inst/doc/Comparisons.Rnw: ditto
595 : maechler 1228
596 : maechler 1226 2006-03-11 Martin Maechler <maechler@stat.math.ethz.ch>
597 :    
598 :     * R/dgCMatrix.R (replCmat): "[<-" methods for dgCMatrix
599 :    
600 :     * tests/indexing.R: tests for new [<- methods for sparse matrices.
601 :    
602 :     2006-03-10 Martin Maechler <maechler@stat.math.ethz.ch>
603 :    
604 :     * R/dgTMatrix.R (replTmat): "[<-" methods for dgTMatrix
605 :    
606 :     * R/Tsparse.R (.ind.prep): fix out-of-range indexing
607 :    
608 :     2006-03-08 Martin Maechler <maechler@stat.math.ethz.ch>
609 :    
610 :     * R/dMatrix.R: enable things like M [ M < 10 ]
611 :     * R/dgeMatrix.R: implement it
612 :    
613 : maechler 1222 2006-03-06 Martin Maechler <maechler@stat.math.ethz.ch>
614 :    
615 :     * R/AllClass.R: define "summary.mer" and "*.lmer"
616 :     * R/lmer.R (summary): summary(<mer>) computes & returns the above;
617 :     * R/lmer.R (show): now works with summary()
618 :    
619 :     2006-03-04 Martin Maechler <maechler@stat.math.ethz.ch>
620 :    
621 :     * R/dgCMatrix.R: finally direct "Arith" dgC o dgC
622 :     * R/Auxiliaries.R (WhichintersectInd): and other utilities to
623 :     support the above
624 :    
625 : bates 1213 2006-02-07 Douglas Bates <bates@stat.wisc.edu>
626 :    
627 :     * R/lmer.R (lmer): fix initial values of offset and weights for glm.fit.
628 :     Use glmFit$prior.weights for weights in a glmm.
629 :     Allow an option usePQL = FALSE to skip the PQL steps for the
630 :     Laplace method (and, in time, the AGQ method).
631 :    
632 :     * src/lmer.c (mer_factor): Move downdating and factoring of XtX
633 :     into a separate function internal_mer_Xfactor to be able to call
634 :     it from internal_bhat.
635 :    
636 : maechler 1200 2006-01-23 Martin Maechler <maechler@stat.math.ethz.ch>
637 :    
638 :     * tests/Class+Meth.R (tstMatrixClass): function for much better
639 :     testing; now again of all actual classes.
640 :    
641 :     * src/Mutils.c (MAKE_TRIANGULAR_BODY, MAKE_SYMMETRIC_BODY):
642 :     use macros and define make_d_matrix_* and make_i_matrix_*
643 :     where _i_ is for the ldense routines:
644 :    
645 :     * src/ldense.c (ltrMatrix_as_lgeMatrix): provide functions
646 :     * src/ldense.c (lsyMatrix_as_lgeMatrix):
647 :    
648 :     * R/ldenseMatrix.R: use the above in setAs(*,"lgeMatrix")
649 :    
650 :    
651 : maechler 1174 2006-01-16 Martin Maechler <maechler@stat.math.ethz.ch>
652 :    
653 :     * R/Matrix.R (Matrix): has become much "smarter" now auto-producing
654 :     many different kinds of matrices.
655 :     * R/*.R: quite a few new methods were needed for R CMD check with
656 :     new Matrix(). Very good for users playing around.
657 :    
658 :    
659 : maechler 1165 2006-01-15 Martin Maechler <maechler@stat.math.ethz.ch>
660 :    
661 :     * src/dgeMatrix.c (dMatrix_validate): new
662 :     * src/Mutils.c (dense_nonpacked_validate): new
663 :    
664 :     * src/dtrMatrix.c (dtrMatrix_validate): improved/fixed
665 :    
666 :    
667 :     2006-01-14 Douglas Bates <bates@stat.wisc.edu>
668 :    
669 :     * R/AllClass.R (compMatrix), (generalMatrix): new virtual classes
670 :    
671 : bates 1123 2006-01-07 Douglas Bates <bates@stat.wisc.edu>
672 : bates 1119
673 : maechler 1127 * DESCRIPTION (Version): 0.99-6 released to CRAN
674 :    
675 : bates 1119 * src/dgBCMatrix.c (cscb_trcbsm): Fix due to Peter Dalgaard for
676 :     segfault in cases with multiple non-nested grouping factors.
677 :    
678 : maechler 1109 2006-01-03 Martin Maechler <maechler@stat.math.ethz.ch>
679 :    
680 :     * DESCRIPTION (Version): 0.99-4 to be released to CRAN
681 :     (Depends): also on 'utils'
682 :    
683 :     * R/AllClass.R (diagonalMatrix): new class with "ddi*" and "ldi*"
684 :     * R/diagMatrix.R (Diagonal): constructor and methods for
685 :     diagonal matrices
686 :    
687 :     * R/ltTMatrix.R: new "minimal methods"
688 :    
689 : maechler 1091 2005-12-12 Martin Maechler <maechler@stat.math.ethz.ch>
690 :    
691 :     * R/AllGeneric.R (tcrossprod): 2-argument version; here, and for
692 :     all methods (and help files).
693 :    
694 : maechler 1084 2005-12-09 Martin Maechler <maechler@stat.math.ethz.ch>
695 :    
696 :     * R/Auxiliaries.R (dimNamesCheck): fixed thinko -> bug
697 :     for case (dimn. op no_dimn.)
698 :    
699 :     2005-11-14 Douglas Bates <bates@stat.wisc.edu>
700 :    
701 : maechler 1174 * DESCRIPTION (Version): 0.99-2 released to CRAN
702 : maechler 1084
703 : bates 988 2005-10-21 Douglas Bates <bates@stat.wisc.edu>
704 :    
705 :     * R/lmer.R (simulate method): Fixed a drop=FALSE problem reported
706 :     by Julian Faraway.
707 :    
708 : maechler 976 2005-10-06 Martin Maechler <maechler@stat.math.ethz.ch>
709 :    
710 :     * R/Auxiliaries.R (try_as): new utility
711 :     * R/sparseMatrix.R: use try_as() in coercion to original class
712 :    
713 : maechler 956 2005-09-30 Martin Maechler <maechler@stat.math.ethz.ch>
714 :    
715 :     * src/dgCMatrix.c (double_to_csc): and dgeMatrix_to_csc()
716 :    
717 :     2005-09-29 Martin Maechler <maechler@stat.math.ethz.ch>
718 :    
719 :     * R/Auxiliaries.R (dimNamesCheck): added
720 :    
721 :     * R/Matrix.R (as.array), (as.vector): new
722 :    
723 : maechler 954 2005-09-28 Martin Maechler <maechler@stat.math.ethz.ch>
724 :    
725 :     * R/Matrix.R (Matrix): get logical argument 'sparse' with a smart
726 : maechler 956 default.
727 :     * R/AllClass.R: move 'factors' slot toplevel "Matrix";
728 :     "pMatrix" now contains "sparseMatrix"
729 : maechler 954
730 : maechler 948 2005-09-26 Martin Maechler <maechler@stat.math.ethz.ch>
731 :    
732 :     * tests/Class+Meth.R: new tests; t(t(m)) == m
733 :    
734 :     * src/dtCMatrix.c (tsc_transpose): add forgotten "diag" slot
735 :    
736 :     * src/dsTMatrix.c (dsTMatrix_as_dsCMatrix): bad typo (segfault!)
737 :     * src/dtTMatrix.c (dtTMatrix_as_dtCMatrix): new
738 :    
739 :     * R/dspMatrix.R: typo in "t" method
740 :    
741 : maechler 925 2005-09-18 Douglas Bates <bates@wisc.edu>
742 :    
743 :     * R/AllClass.R (TsparseMatrix), CsparseM* and RsparseM*
744 :     * R/Tsparse.R: instead of R/gTMatrix.R
745 :     * R/Csparse.R: new
746 :     * src/Tsparse.c (Tsparse_to_Csparse): new; -> cholmod_()
747 :     * src/Tsparse.c: new; many trivial methods calling cholmod_()
748 :     * src/Csparse.c (Csparse_to_Tsparse), transpose, (mat|cross)prod:
749 :     via cholmod
750 :    
751 :     2005-09-16 Martin Maechler <maechler@stat.math.ethz.ch>
752 :    
753 :     * R/Auxiliaries.R (non0ind): new function using new C code
754 :     * src/dgCMatrix.c (compressed_non_0_ij): new utility
755 :    
756 : bates 917 2005-09-15 Douglas Bates <bates@localhost.localdomain>
757 :    
758 :     * src/chm_common.h: header file required by all C sources that
759 : maechler 1174 call CHOLMOD functions. It defines a cholmod_common structure
760 : bates 917 called 'c' whose address is passed as the last argument to
761 :     (virtually) every CHOLMOD function.
762 :    
763 :     * src/Pattern.c: Simple example of the use of CHOLMOD.
764 :    
765 :     * src/init.c: initialize and finalize the cholmod_common structure.
766 :    
767 :     * src/Makefile: Added source packages CHOLMOD UMFPACK AMD COLAMD
768 :     LDL and CCOLAMD from the U. of Florida sparse matrix library.
769 :    
770 : maechler 908 2005-09-08 Martin Maechler <maechler@stat.math.ethz.ch>
771 :    
772 :     * inst/test-tools.R: new file collecting the utility functions used
773 :     in ./tests/*.R
774 :    
775 :     * R/ddenseMatrix.R (cbind2): new methods for "numeric" and "matrix"
776 :     * R/Matrix.R (cbind2): methods for NULL and missing
777 :    
778 : maechler 886 2005-08-31 Martin Maechler <maechler@stat.math.ethz.ch>
779 :    
780 :     * R/AllClass.R: new "index" class for "[" and "[<-":
781 :     First cut at "symmetricMatrix" and "triangularMatrix"
782 :     * R/gTMatrix.R (.ind.prep): new function;
783 : maechler 1174 Logical and character indexing now work too.
784 : maechler 886 * R/Matrix.R: cheap "[<-" methods for denseMatrix now work
785 :     * tests/indexing.R: new, including *.Rout.save
786 :     * tests/dgTMatrix.R: new
787 :    
788 : bates 876 2005-08-29 Douglas Bates <bates@wisc.edu>
789 :    
790 :     * src/dgTMatrix.c (graphNEL_as_dgTMatrix): Corrected the position
791 :     indicator pos not being updated. Also enforced upper triangular
792 :     for symmetric case. Need to coerce edges component of elements of
793 :     edge list - grr! (Why don't they define their classes cleanly?)
794 :    
795 : maechler 871 2005-08-26 Martin Maechler <maechler@stat.math.ethz.ch>
796 :    
797 :     * R/Matrix.R: added first "[<-" methods; not yet functional
798 : bates 1352 * R/denseMatrix.R: ditto
799 : maechler 871 * man/Subassign-methods.Rd: new help file for these
800 :    
801 :     2005-08-25 Martin Maechler <maechler@stat.math.ethz.ch>
802 :    
803 :     * DESCRIPTION (Version): 0.98-6
804 :    
805 :     * R/denseMatrix.R: new file for "[" fallback methods for all dense
806 :     matrices.
807 :    
808 : maechler 868 2005-08-19 Martin Maechler <maechler@stat.math.ethz.ch>
809 :    
810 :     * src/lgCMatrix.c (lcsc_to_matrix): new; need for
811 :     as( <logical>, "matrix")
812 :    
813 :     * R/pMatrix.R: coercion to "lgTMatrix"
814 :    
815 :     * R/gTMatrix.R: new virtual class to define "[" methods for.
816 :     * man/gTMatrix-class.Rd:
817 :     * General slight re-organization of where "[" methods are defined.
818 :     more to come.
819 :    
820 : maechler 871 2005-08-18 Douglas Bates <bates@wisc.edu>
821 : maechler 868
822 : maechler 1174 * DESCRIPTION (Version): 0.98-5 released to CRAN
823 : maechler 871
824 :     * src/dgTMatrix.c (graphNEL_as_dgTMatrix): add first graphNEL methods
825 :     * .....
826 :    
827 : bates 863 2005-08-18 Douglas Bates <bates@localhost.localdomain>
828 :    
829 :     * R/lmer.R: Corrected naming scheme in mcmcsamp to work with lmer
830 :     or glmer objects.
831 :    
832 : maechler 860 2005-08-17 Martin Maechler <maechler@stat.math.ethz.ch>
833 :    
834 :     * DESCRIPTION (Version): 0.98-4 : upload to CRAN
835 :    
836 :     2005-08-16 Douglas Bates <bates@localhost.localdomain>
837 :    
838 :     * R/HBMM.R: finish re-writing R-only code.
839 :    
840 : bates 854 2005-08-15 Douglas Bates <bates@localhost.localdomain>
841 :    
842 :     * man/externalFormats.Rd: move documentation for writeHB and
843 :     writeMM here.
844 :    
845 :     * src/mmio.c: replace inclusion of <malloc.h> by <stdlib.h>
846 :     (suggested by Paul Roecker).
847 :    
848 :     * tests/validObj.R (assertError): Comment out test that is failing
849 :     after recent changes in r-devel.
850 :    
851 : maechler 860
852 : maechler 848 2005-08-11 Martin Maechler <maechler@stat.math.ethz.ch>
853 :    
854 :     * R/AllClass.R: intermediate virtual class "denseMatrix"
855 :     * man/denseMatrix-class.Rd
856 :     * NAMESPACE: export it, and also export
857 :     * man/unused-classes.Rd: "iMatrix", "zMatrix" and "ldenseMatrix"
858 :    
859 : bates 846 2005-08-10 Douglas Bates <bates@wisc.edu>
860 :    
861 : maechler 848 * DESCRIPTION (Version): 0.98-3 to CRAN
862 :    
863 : bates 846 * src/dtrMatrix.c (dtrMatrix_validate): fixed up validation and
864 :     matrix_solve code (which was really, really wrong).
865 :    
866 : bates 835 2005-08-07 Douglas Bates <bates@wisc.edu>
867 : maechler 834
868 :     * DESCRIPTION (Version): 0.98-2
869 :    
870 :     * R/HBMM.R (readHB), (readMM): read Matrix Market formats
871 :    
872 :     * R/lmer.R (abbrvNms): new
873 :     * R/lmer.R (mcmcsamp): allow transformed parameters
874 : bates 835 * src/HBMM.c (Matrix_writeMatrixMarket): Added read/write routines
875 :     for the Harwell-Boeing and the MatrixMarket formats.
876 : maechler 834
877 :     2005-08-04 Martin Maechler <maechler@stat.math.ethz.ch>
878 :    
879 :     * man/dtrMatrix-class.Rd: add examples
880 : bates 835 * man/dtpMatrix-class.Rd: ditto; plus note about PROBLEM
881 : maechler 834
882 :     * TODO: note the dtpMatrix (docu) bug
883 :    
884 :     * R/zzz.R (.onLoad): assignInNamespace("as.matrix", *, "base")
885 :     in order to ensure that new as.matrix() is used by old functions,
886 :     e.g., svd(), qr(), eigen(), dist(),..;
887 :     apply(), also matplot() or pairs().
888 :    
889 :    
890 :     2005-08-03 Martin Maechler <maechler@stat.math.ethz.ch>
891 :    
892 :     * R/lmer.R: add 'fixme' comments and move the linear vs glm check;
893 :     add comments about 'control' / lmerControl() arguments
894 :    
895 : bates 835 2005-07-27 Douglas Bates <bates@wisc.edu>
896 : bates 820
897 : bates 835 * man/sleepstudy.Rd: Added the sleep data set.
898 : maechler 1174 * DESCRIPTION (Version): 0.98-1 released to CRAN
899 : bates 820
900 : bates 835 2005-07-12 Douglas Bates <bates@wisc.edu>
901 : maechler 834 * man/sleepstudy.Rd: Added the sleep data set.
902 :    
903 : bates 809 * R/lmer.R (glmmMCMC): Added PACKAGE = "Matrix" in a couple of
904 :     .Call calls that were producing spurious output.
905 :    
906 : bates 835 2005-07-05 Douglas Bates <bates@wisc.edu>
907 : bates 801
908 :     * R/lmer.R (lmer): stored updated variance component estimates in
909 :     mer object for the generalized model. (Bug reported by Renaud
910 :     Lancelot).
911 :    
912 : bates 835 2005-07-03 Douglas Bates <bates@wisc.edu>
913 : bates 794
914 :     * src/lmer.c (glmer_devAGQ): Added AGQ for single grouping factor,
915 :     unidimensional case.
916 :    
917 : bates 835 2005-06-08 Douglas Bates <bates@wisc.edu>
918 : maechler 791
919 :     * DESCRIPTION (Version): 0.96-1
920 :    
921 : maechler 1174 * moved lmer-class' R and C code moved from lme4 to here
922 : maechler 791
923 : bates 835 2005-06-04 Douglas Bates <bates@wisc.edu>
924 : bates 763
925 :     * R/dgCMatrix.R: Call to csc_matrix_mm used undefined arguments
926 :     (reported by Guissepe Ragusa <gragusa@ucsd.edu>)
927 :    
928 : bates 835 2005-06-02 Douglas Bates <bates@wisc.edu>
929 : bates 763
930 :     * src/Makefile.win: Forgot to update this when Makefile changed.
931 :    
932 : bates 835 2005-05-11 Douglas Bates <bates@wisc.edu>
933 : bates 726
934 :     * src/dgCMatrix.c (csc_transpose): Simplified function fixing a
935 :     bug reported by Kurt Hornik and Michael Hahsler.
936 :    
937 : bates 835 2005-05-10 Douglas Bates <bates@wisc.edu>
938 : bates 725
939 :     * src/lgCMatrix.c (Matrix_lgClgCmm): Implementation of methods for
940 :     logical sparse matrices. These will also be used in the symbolic
941 :     analysis for lmer objects.
942 :    
943 :     * src/dsCMatrix.c (dsCMatrix_matrix_solve): Copied the dimensions
944 :     of b to the result. Fixes bug reported by Jean.Coursol@math.u-psud.fr
945 : maechler 791
946 : bates 835 2005-05-06 Douglas Bates <bates@wisc.edu>
947 : bates 714
948 :     * src/dgeMatrix.c (dgeMatrix_colsums): Added an implementation of
949 :     colMeans, colSums, rowMeans and rowSums.
950 :    
951 : bates 835 2005-04-18 Douglas Bates <bates@wisc.edu>
952 : bates 692
953 :     * src/lgCMatrix.[ch]: code for _validate method and stub for
954 :     multiplication operation.
955 :    
956 :     * src/dgeMatrix.c (dgeMatrix_matrix_solve): Passing wrong argument
957 :     to dgetrs.
958 :    
959 :     * src/init.c: Fix cut-and-paste error in definition of
960 :     dgeMatrix_matrix_solve
961 :    
962 :     * src/{many files}: Tighten code by using ALLOC_SLOT.
963 :    
964 : bates 835 2005-04-15 Douglas Bates <bates@wisc.edu>
965 : bates 692
966 :     * R/AllClass.R: Add lgTMatrix and lgCMatrix classes
967 :    
968 :     * DESCRIPTION: Eliminate import of stats.
969 :    
970 : maechler 791
971 : bates 835 2005-04-06 Douglas Bates <bates@wisc.edu>
972 : bates 692
973 :     * R/AllClass.R : add logical sparse matrix classes
974 :    
975 : maechler 687 2005-04-01 Martin Maechler <maechler@stat.math.ethz.ch>
976 :    
977 :     * R/dgTMatrix.R: add "[" method for triplet matrices
978 :     * R/sparseMatrix.R: and other sparse ones; --> add show() for sparse
979 :    
980 : bates 835 2005-03-31 Douglas Bates <bates@wisc.edu>
981 : maechler 687
982 :     * DESCRIPTION (Version): release 0.95-5 to CRAN
983 :    
984 :     * R/dMatrix.R: add %*%, crossprod and solve "fallback" methods
985 :     * R/sparseMatrix.R: %*%, crossprod()
986 :     * R/dgeMatrix.R: more "fallback" methods for numeric/dense matrices
987 :     * man/*.Rd: move method definitions to 'Matrix' and 'dMatrix'
988 :     * src/lmer.c (lmer_fitted): fix thinko
989 :    
990 : maechler 676 2005-03-26 Martin Maechler <maechler@stat.math.ethz.ch>
991 :    
992 :     * R/AllClass.R: add two virtual sparse classes ``on top''
993 :    
994 :     2005-03-24 Martin Maechler <maechler@stat.math.ethz.ch>
995 :    
996 :     * R/AllClass.R (setClass): use "VIRTUAL" for the virtual classes;
997 :     correspondingly fix examples and tests/ since new()
998 :     doesn't work for virtual classes.
999 :    
1000 : maechler 658 2005-03-17 Martin Maechler <maechler@stat.math.ethz.ch>
1001 :    
1002 :     * R/Matrix.R (as.matrix): method and one for unname()
1003 :     * tests/dpoMatrix.R: tests should now be less platform dependent;
1004 :     also run for R 2.1.0; using as.matrix()
1005 :    
1006 : bates 835 2005-03-15 Douglas Bates <bates@wisc.edu>
1007 : maechler 658
1008 :     * R/pMatrix.R: "pMatrix" class added
1009 :     * ....
1010 :    
1011 : bates 835 2005-03-14 Douglas Bates <bates@wisc.edu>
1012 : bates 645
1013 :     * R/dtpMatrix.R: Add unpack method and an example.
1014 :    
1015 :     * src/dsyMatrix.c (dsyMatrix_trf): Add BunchKaufman factorization
1016 :     of general symmetric matrices and associated S4 methods.
1017 :    
1018 : maechler 658 2005-03-10 Martin Maechler <maechler@stat.math.ethz.ch>
1019 :     +
1020 :     2005-03-05 Martin Maechler <maechler@stat.math.ethz.ch>
1021 :    
1022 :     * R/dgeMatrix.R (setAs): and many other files: more coercion,
1023 :     crossprod() and "%*%" methods added; tests, too.
1024 :     * tests/matprod.R: new, for testing these
1025 :    
1026 : bates 835 2005-03-03 Douglas Bates <bates@wisc.edu>
1027 : bates 599
1028 :     * src/lmer.c (lmer_fitted): Added.
1029 :    
1030 : bates 835 2005-03-02 Douglas Bates <bates@wisc.edu>
1031 : bates 596
1032 :     * R/dsTMatrix.R: Conversion from dsTMatrix to dsCMatrix
1033 :    
1034 : bates 835 2005-02-28 Douglas Bates <bates@wisc.edu>
1035 : bates 582
1036 :     * src/*.c,po/,inst/po: Internationalization and localization of
1037 :     the package.
1038 :    
1039 :     * src/ldl.[ch]: Removed these as their contents are referenced in the
1040 :     R_ldl.c file.
1041 :    
1042 :     * src/flame.[ch]: Removed these source files.
1043 : maechler 658
1044 : bates 582 * src/dtrMatrix.c (make_array_triangular): Move to Mutils
1045 :    
1046 :     * src/LU.[ch],src/init.c: absorb in factorizations
1047 :    
1048 :     * src/Mutils.h: prepare for internationalization
1049 :    
1050 :     * src/cblas.h: move the enum definitions to Mutils.h and remove
1051 :     this file
1052 :    
1053 : maechler 578 2005-02-26 Martin Maechler <maechler@stat.math.ethz.ch>
1054 :    
1055 : maechler 579 * R/dgeMatrix.R: provide "dimnames" and "dimnames<-" methods
1056 :    
1057 :     * R/dtrMatrix.R: fix t() method
1058 :    
1059 : maechler 578 * R/dgeMatrix.R: define group methods "Arith", "Math", "Math2"
1060 : maechler 658 * NAMESPACE: export them (and import generics from "methods")
1061 : maechler 578 * tests/group-methods.R : and test them.
1062 :    
1063 :     * src/dtrMatrix.c (dtrMatrix_as_dgeMatrix): prevent seg.fault in
1064 :     border case
1065 :    
1066 :     2005-02-24 Douglas Bates <bates@stat.wisc.edu>
1067 :    
1068 : maechler 658 * DESCRIPTION (Version): 0.95-2 released to CRAN
1069 : maechler 578
1070 :     * src/dgBCMatrix.c:
1071 :     * src/lmer.c: many changes
1072 :     * ...
1073 :    
1074 : maechler 512 2005-02-04 Martin Maechler <maechler@stat.math.ethz.ch>
1075 :    
1076 :     * R/Matrix.R: add more sophisticated show() method.
1077 :    
1078 : maechler 578 2005-02-02 Douglas Bates <bates@stat.wisc.edu>
1079 :    
1080 :     * */* : almost complete reorganization of classes.
1081 :    
1082 : bates 835 2005-01-26 Douglas Bates <bates@wisc.edu>
1083 : bates 460
1084 :     * R/AllGeneric.R: Added matrix exponential generic expm and a method
1085 :     for the geMatrix class.
1086 :    
1087 : bates 835 2005-01-24 Douglas Bates <bates@wisc.edu>
1088 : bates 460
1089 :     * src/Makefile (clean): Remove *.a and *.so
1090 :    
1091 :     * man/cscBlocked-class.Rd: Remove reference to the lmer-class.
1092 :    
1093 : bates 835 2005-01-23 Douglas Bates <bates@wisc.edu>
1094 : bates 460
1095 : maechler 658 * src/lmer.c (Lind): Definition of Lind was backwards. This only
1096 : bates 460 had an effect in cases with more than 2 grouping factors.
1097 :    
1098 : bates 835 2005-01-03 Douglas Bates <bates@wisc.edu>
1099 : bates 415
1100 :     * src/lmeRep.c (lmer_variances): change from lmeRep to lmer
1101 :    
1102 : bates 835 2004-12-23 Douglas Bates <bates@wisc.edu>
1103 : bates 410
1104 :     * src/init.c (R_init_Matrix): Reorder calls to R_registerRoutines
1105 :     and R_useDynamicSymbols (suggested by B.D.Ripley).
1106 :    
1107 : bates 835 2004-12-14 Douglas Bates <bates@wisc.edu>
1108 : bates 392
1109 :     * R/sscMatrix.R: Add determinant methods
1110 :    
1111 :     * src/triplet.[ch],src/init.c (triplet_to_matrix): Add a coercion
1112 :     for tripletMatrix to matrix.
1113 :    
1114 : bates 835 2004-12-13 Douglas Bates <bates@wisc.edu>
1115 : bates 388
1116 : bates 392 * R/AllClass.R (.onLoad): Eliminate the bbCrosstab class, which is
1117 :     no longer used.
1118 :    
1119 : bates 388 * src/R_ldl.c: Created an R-specific version of the ldl.[ch] files
1120 :     with dynamic allocation of scratch arrays.
1121 :    
1122 :     * src/ssclme.c (ssclme_copy_ctab): Fixed bug in creation of ZtZ
1123 :     for multivariate random effects with multiple grouping factors.
1124 :     Fixes part but not all of #15.
1125 :    
1126 : bates 835 2004-12-03 Douglas Bates <bates@wisc.edu>
1127 : bates 375
1128 :     * src/lmeRep.c (lmeRep_factor): order of operations for multiple
1129 :     scalar grouping factors corrected.
1130 :    
1131 : bates 835 2004-11-29 Douglas Bates <bates@wisc.edu>
1132 : bates 375
1133 :     * src/bCrosstab.c: remove diag_update which is no longer used
1134 :    
1135 : bates 835 2004-11-16 Douglas Bates <bates@wisc.edu>
1136 : bates 350
1137 :     * src/Metis_utils.c: Move metis.h include to C sources so that the
1138 :     .h file can be included.
1139 :    
1140 : bates 835 2004-11-12 Douglas Bates <bates@wisc.edu>
1141 : bates 342
1142 : bates 350 * src/LU.c,geMatrix.c,trMatrix.c, etc.:
1143 : bates 342 Complete allocation of slots in NEW_OBJECT.
1144 :    
1145 :     * src/Mutils.h: Moved list of symbols to an include file
1146 :    
1147 : bates 835 2004-11-11 Douglas Bates <bates@wisc.edu>
1148 : bates 342
1149 :     * src/geMutils.c (Matrix_init): remove unused function
1150 :    
1151 : bates 835 2004-11-10 Douglas Bates <bates@wisc.edu>
1152 : bates 342
1153 :     * src/cscMatrix.c (csc_to_imagemat): removed unused function
1154 :    
1155 : bates 835 2004-11-05 Douglas Bates <bates@wisc.edu>
1156 : bates 327
1157 :     * src/Makefile.win (SOURCES_C): Keep consistent with Makefile
1158 :    
1159 : bates 835 2004-10-27 Douglas Bates <bates@wisc.edu>
1160 : bates 303
1161 :     * R/pdmatrix.R: remove PACKAGE="Matrix" in .Call calls
1162 :    
1163 : bates 835 2004-10-04 Douglas Bates <bates@wisc.edu>
1164 : bates 296
1165 :     * src/init.c: Created R_init_Matrix and added registration of C
1166 :     routines.
1167 :    
1168 : bates 835 2004-10-02 Douglas Bates <bates@wisc.edu>
1169 : bates 283
1170 :     * R/tripletMatrix.R: Force a require(lattice) for the image methods.
1171 :    
1172 : bates 835 2004-06-15 Douglas Bates <bates@wisc.edu>
1173 : bates 229
1174 :     * man/trMatrix-class.Rd: Escape the % chars in .Rd files.
1175 :    
1176 : bates 111 2004-04-20 Douglas Bates <bates@stat.wisc.edu>
1177 :    
1178 :     * src/Makefile.win ($(SHLIB)): Modifications per Uwe Ligges.
1179 :    
1180 : bates 109 2004-04-19 Douglas Bates <bates@stat.wisc.edu>
1181 :    
1182 :     * src/ssclme.c (ssclme_update_mm): fix logic error in
1183 :     ssclme_update_mm
1184 :    
1185 : bates 105 2004-04-18 Douglas Bates <bates@stat.wisc.edu>
1186 :    
1187 :     * src/ssclme.c (ssclme_coef, ssclme_coefGets): Create consistency
1188 :     in the order of unconstrained and constrained parameters.
1189 :     (ssclme_gradient): Added the gradients (not yet correct for
1190 :     multidimensional, unconstrained case).
1191 :    
1192 : bates 78 2004-04-14 Douglas Bates <bates@stat.wisc.edu>
1193 :    
1194 :     * src/ssclme.c (ssclme_EMsteps): Fix logic in REML update
1195 :    
1196 :     * src/Makefile.win: Remove unneeded ranlib call
1197 :    
1198 : bates 71 2004-04-12 Douglas Bates <bates@stat.wisc.edu>
1199 :    
1200 :     * DESCRIPTION (Version): New release
1201 :    
1202 :     * src/Makefile.win: Update Makefile.win to umfpack removal.
1203 :    
1204 : bates 49 2004-04-05 Douglas Bates <bates@bates2_home>
1205 :    
1206 :     * src/triplet_to_col.c: Create triplet_to_col as a native
1207 : maechler 658 function, not the version from umfpack. There were problems with
1208 : bates 49 the configuration of UMFPACK for 64-bit processors and there was
1209 :     only one umfpack routine being used so I moved it here.
1210 :    
1211 : bates 45 2004-04-04 Douglas Bates <bates@bates2_home>
1212 :    
1213 :     * src/ssclme.c (ssclme_variances): New function.
1214 :    
1215 : bates 28 2004-03-28 Douglas Bates <bates@bates2_home>
1216 :    
1217 :     * src/ssclme.c (ssclme_fitted): Added function.
1218 :    
1219 : bates 22 2004-03-27 Douglas Bates <bates@bates2_home>
1220 :    
1221 :     * src/ssclme.c (ssclme_transfer_dimnames): Add new function to
1222 :     store the dimnames in the XtX and bVar slots
1223 :     (ssclme_update_mm): Change the dimensions of the bVar slot
1224 :     components and the returned value from ssclme_ranef.
1225 :    
1226 : bates 10 2004-03-18 Douglas Bates <bates@stat.wisc.edu>
1227 :    
1228 :     * R/{pdMat.R,pdIdent.R,pdLogChol.R,pdMatrixLog.R,pdNatural.R},
1229 :     src/{pdMat.c,pdIdent.c,pdLogChol.c,pdNatural.c},
1230 :     tests/{pdCompSymm.R,pdDiag.R,pdIdent.R,pdLogChol.R,pdNatural.R},
1231 :     man/{pdMat-class.Rd,pdmatrix-class.Rd,corrmatrix-class.Rd,
1232 :     pdDiag-class.Rd,pdIdent-class.Rd,pdNatural-class.Rd,
1233 :     pdLogChol-class.Rd,coefGets.Rd,pdCompSymm-class.Rd,
1234 :     pdfactor-class.Rd,pdFactor.Rd,pdMatrix.Rd,
1235 :     pdBlocked-class.Rd},AllClass.R,AllGeneric.R:
1236 :     Moved the pdMat classes from the lme4 package.
1237 :    
1238 :     2004-03-02 Douglas Bates <bates@stat.wisc.edu>
1239 :    
1240 :     * man/ssclme-class.Rd: Update definition and documentation of the
1241 :     ssclme class to include the DIsqrt slot.
1242 :    
1243 :     * src/ssclme.c (ssclme_deviance): Modify order of computation
1244 :     (much faster using dsyrk, a level 3 BLAS routine).
1245 :    
1246 :     * src/Makefile (SUBLIBS): Change definition (K. Hornik)
1247 :    
1248 :     2004-02-28 Douglas Bates <bates@stat.wisc.edu>
1249 :    
1250 :     * tests/ssclme.R: Modify the test to account for the permutation
1251 :     of the levels of the grouping factors.
1252 :    
1253 :     2004-02-23 Douglas Bates <bates@stat.wisc.edu>
1254 :    
1255 :     * R/ssclme.R,src/ssclme.c (ssclme): Move slots of sscCrosstab slot
1256 :     directly into the ssclme class definition.
1257 :    
1258 :     2004-02-22 Douglas Bates <bates@stat.wisc.edu>
1259 :    
1260 :     * DESCRIPTION (Date): New release
1261 :    
1262 :     * man/ssclme-class.Rd: new file.
1263 :    
1264 :     * src/ssclme.c (ssclme_loglik): major revisions in design. It
1265 :     works and it's fast!
1266 :    
1267 :     2004-02-17 Douglas Bates <bates@stat.wisc.edu>
1268 :    
1269 :     * src/taucs/Makefile.win (lib): Change "ar" to "$(AR)" (B.Ripley)
1270 :    
1271 :     2004-02-16 Douglas Bates <bates@stat.wisc.edu>
1272 :    
1273 :     * DESCRIPTION (Date): New release
1274 :    
1275 :     * NAMESPACE: Don't export ssclme.
1276 :    
1277 :     * data/ScotsSec.rda, man/ScotsSec.Rd: Add Scottish secondary
1278 :     school data.
1279 :    
1280 :     2004-02-11 Douglas Bates <bates@stat.wisc.edu>
1281 :    
1282 :     * src/sscCrosstab.c (sscCrosstab): Added a row to the incidence to
1283 :     keep track of the fixed-effects and the response. Counts also
1284 :     gets an extra element, which is always one.
1285 :    
1286 :     * src/ldl.c: Include these routines from Tim Davis' LDL package.
1287 :    
1288 :     2004-02-10 Douglas Bates <bates@stat.wisc.edu>
1289 :    
1290 :     * src/cscMatrix.c (csc_transpose): new function
1291 :    
1292 :     * src/Mutils.c (csc_sort_columns): perm/iperm confusion corrected
1293 :     (csc_components_transpose): new function
1294 :    
1295 :     2004-02-06 Douglas Bates <bates@stat.wisc.edu>
1296 :    
1297 :     * src/triplet.c (triplet_validate): Fix Dim slot on generated
1298 :     triplets
1299 :    
1300 :     2004-01-30 Douglas Bates <bates@stat.wisc.edu>
1301 :    
1302 :     * R/sscCrosstab.R (sscCrosstab): Added sscCrosstab generator function.
1303 :    
1304 :     * src/LU.h (MATRIX_LU_H): Add #ifndef #define ... #endif to this
1305 :     and all other .h files in src.
1306 :    
1307 :     * src/Makefile.win: This and other Makefile.win files contributed
1308 :     by Brian Ripley.
1309 :    
1310 :     2004-01-27 Douglas Bates <bates@stat.wisc.edu>
1311 :    
1312 :     * R/syMatrix.R: Added methods for "%*%".
1313 :    
1314 :     * R/Hilbert.R (Hilbert): Changed Hilbert function to return a
1315 :     poMatrix object.
1316 :    
1317 :     2004-01-26 Douglas Bates <bates@stat.wisc.edu>
1318 :    
1319 :     * man/sscChol-class.Rd,man/mm.Rd,man/y.Rd: Added man pages.
1320 :    
1321 :     2004-01-25 Douglas Bates <bates@bates2_home>
1322 :    
1323 :     * inst/doc/Introduction.Rnw,Comparisons.Rnw: Added vignettes.
1324 :    
1325 :     * R/csc.R: Convert all cscMatrix classes to use Dim slot instead
1326 :     of nrow.
1327 :    
1328 :     2003-12-31 Douglas Bates <bates@stat.wisc.edu>
1329 :    
1330 :     * src/taucs/taucs.h: Moved taucs.h, amd.h, and umfpack.h into
1331 :     subdirectories.
1332 :    
1333 :     2003-12-08 Douglas Bates <bates@stat.wisc.edu>
1334 :    
1335 :     * src/taucs.h: Accidently referred to global header files
1336 :     instead of local files.
1337 :    
1338 :     2003-12-04 Douglas Bates <bates@stat.wisc.edu>
1339 :    
1340 :     * R/AllClass.R: Lots of changes. Removed all the lapack++ code
1341 :     and methods and replaced all classes with S4 classes.
1342 :    
1343 :     2003-04-19 Douglas Bates <bates@stat.wisc.edu>
1344 :    
1345 :     * R/det.R,man/det.Rd: Change name of det generic to determinant
1346 :    
1347 :     * src/R_LapackPP.cc: Change method of calculating determinants
1348 :    
1349 :     2003-02-03 Douglas Bates <bates@stat.wisc.edu>
1350 :    
1351 :     * DESCRIPTION (Version): removed empty data directory as requested
1352 :     by CRAN maintainers. Changed version number and date.
1353 :    
1354 :     2002-10-23 Douglas Bates <bates@stat.wisc.edu>
1355 :    
1356 :     * src/laindex.h: Applied patches from Brian Ripley for compilation
1357 :     under Windows.
1358 :    
1359 :     * Added configure.win and src/Makevars.win as requested by Brian
1360 :     Ripley.
1361 :    
1362 :     2002-05-03 Douglas Bates <bates@stat.wisc.edu>
1363 :    
1364 :     * src/lamatrix.h: Removing pre-1.2.0 compatibility code per Kurt
1365 :     Hornik.
1366 :    
1367 :     2002-04-24 Douglas Bates <bates@stat.wisc.edu>
1368 :    
1369 :     * configure.ac: Replaced configure.in with configure.ac
1370 :     contributed by Kurt Hornik.
1371 :    
1372 :     * aclocal.m4 (ac_clean_files): Replaced this with Kurt Hornik's
1373 :     version for R-1.5.0
1374 :    
1375 : maechler 512
1376 : bates 10 2001-12-10 Douglas Bates <bates@stat.wisc.edu>
1377 :    
1378 :     * man/eigen.Rd: Removed the .Alias in the example

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