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Annotation of /pkg/ChangeLog

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

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