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

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