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

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