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Annotation of /pkg/ChangeLog

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Revision 2011 - (view) (download)

1 : maechler 2011 2007-07-20 Martin Maechler <maechler@stat.math.ethz.ch>
2 :    
3 :     * R/dMatrix.R: fix from Brian for Math2(., digits = "missing")
4 :     * tests/group-methods.R: and regression-test it
5 :    
6 : bates 2008 2007-07-19 19:45 Douglas Bates <bates@stat.wisc.edu>
7 :    
8 :     * [r4642] inst/include/Matrix.h, inst/include/Matrix_stubs.c,
9 :     inst/include/cholmod.h, src/chm_common.c, src/init.c: Export
10 :     triplet_to_sparse, documentation, use typedefs
11 : maechler 2011
12 : maechler 2005 2007-07-18 Martin Maechler <maechler@stat.math.ethz.ch>
13 :    
14 :     * man/dpoMatrix-class.Rd: added 'corMatrix' example
15 :    
16 :     * src/dsyMatrix.[ch] (dsyMatrix_as_matrix): new 'keep_dimnames' arg
17 :     * src/dtrMatrix.[ch] (dtrMatrix_as_matrix): ditto
18 :     * src/init.c, R/dsyMatrix.R, R/dtrMatrix.R, R/lgTMatrix.R: ditto
19 :    
20 :     * R/lsparseMatrix.R: bug fix in "all" method
21 :     * R/Ops.R (.do.Logic.lsparse): "|" bug in borderline case
22 :    
23 :     * R/dsyMatrix.R (coerce->dsTMatrix): (i,j) slots should *not* have names
24 :     * R/ngTMatrix.R (coerce->ngTMatrix): ditto;
25 :     + matrix |-> nMatrix coercion
26 :     * R/pMatrix.R: + setAs() to dMatrix and from nMatrix
27 :     * man/pMatrix-class.Rd: ditto
28 :    
29 :     * R/Matrix.R (Summary): method for non-dMatrix
30 :    
31 :     * tests/Class+Meth.R (extraValid): new check about "dirty" slots
32 :     * tests/Class+Meth.R (tstMatrixClass): test norm(.);
33 :     test all Summary methods.
34 :    
35 :     2007-07-16 Martin Maechler <maechler@stat.math.ethz.ch>
36 :    
37 :     * R/dgeMatrix.R (norm, rcond): methods for 'matrix'
38 :    
39 :     2007-07-14 Martin Maechler <maechler@stat.math.ethz.ch>
40 :    
41 :     * R/sparseMatrix.R (norm): simple methods for sparseMatrix
42 :    
43 :     * R/pMatrix.R (t?crossprod): methods for pMatrix
44 :    
45 : bates 1987 2007-07-10 Douglas Bates <bates@stat.wisc.edu>
46 :    
47 :     * src/dgeMatrix.c (dgeMatrix_colsums): Get the logic straight.
48 :    
49 : bates 1975 2007-07-09 20:45 Douglas Bates <bates@stat.wisc.edu>
50 :    
51 :     * [r4579] src/dgeMatrix.c: Untangle horrible code in dgeMatrix_colsums
52 : maechler 2005 trying to fix a subtle bug - which has been somewhere else.
53 : bates 1975
54 :     2007-07-09 19:43 Martin Maechler <maechler@stat.math.ethz.ch>
55 :    
56 :     * [r4578] src/dgeMatrix.c: "cleaned" dgeMatrix_colsums() - but did not
57 :     solve the bug
58 :    
59 : maechler 1968 2007-07-08 Martin Maechler <maechler@stat.math.ethz.ch>
60 : bates 1964
61 : maechler 1968 * src/dgCMatrix.c (compressed_to_TMatrix):
62 :    
63 :     2007-07-07 Martin Maechler <maechler@stat.math.ethz.ch>
64 :    
65 :     * src/Csparse.c (Rsparse_validate): new, to have some validity
66 :     checking for RsparseMatrix
67 :     * src/dgCMatrix.c (xRMatrix_validate): ditto
68 :     * src/dtCMatrix.c (tRMatrix_validate): ditto
69 :    
70 :     2007-07-07 Douglas Bates <bates@stat.wisc.edu>
71 :    
72 : bates 1964 * [r4567] R/AllClass.R: Slots already in RsparseMatrix were redefined in
73 :     lgRMatrix
74 :     * [r4568] DESCRIPTION: Prepare for bug-fix release
75 : bates 1966 * [r4570] src/CHOLMOD/Check/cholmod_write.c: Include cholmod_matrixops.h
76 :     for declaration of cholmod_symmetry
77 : maechler 1968
78 : maechler 1961 2007-07-06 Martin Maechler <maechler@stat.math.ethz.ch>
79 :    
80 :     * DESCRIPTION (Version): 0.999375 merged into the trunk; ready for
81 :     release.
82 :    
83 : maechler 1960 2007-07-06 14:11 Douglas Bates <bates@stat.wisc.edu>
84 :    
85 :     * [r4559] src/iohb.c, src/iohb.h: Remove Harwell-Boeing input/output
86 :     functions - no longer used
87 :     * [r4560] src/HBMM.c, src/Mutils.c, src/dgTMatrix.c, src/dgeMatrix.c,
88 :     src/dspMatrix.c, src/dsyMatrix.c, src/dtCMatrix.c,
89 :     src/factorizations.c, src/sparseQR.c: Replace most calls to Calloc by
90 :     Alloca
91 :    
92 :     2007-07-06 13:14 Martin Maechler <maechler@stat.math.ethz.ch>
93 :    
94 :     * [r4558] inst/doc/Comparisons.Rnw, src/CHMfactor.c, src/Csparse.c,
95 :     src/Tsparse.c, src/chm_common.c, src/chm_common.h, src/dense.c,
96 :     src/dgCMatrix.c, src/dsCMatrix.c, src/dtTMatrix.c, src/sparseQR.c,
97 :     src/t_gCMatrix_colSums.c: more R_CheckStack()s
98 :    
99 :     2007-07-05 18:12 Douglas Bates <bates@stat.wisc.edu>
100 :    
101 :     * [r4550] inst/include/Matrix.h: Add the macro N_AS_CHM_DN to "alloca"
102 :     the required amount of memory then call M_numeric_as_chm_dense.
103 :     * [r4556] src/Mutils.h, src/dgCMatrix.c: Define and use the Alloca macro
104 :     (like Calloc but calling alloca)
105 :    
106 : maechler 1947 2007-07-05 Martin Maechler <maechler@stat.math.ethz.ch>
107 :    
108 :     * R/sparseMatrix.R (printSpMatrix): renamed from prSpMatrix()
109 :     and extended with more sophisticated 'col.names' option.
110 :     * NAMESPACE: export printSparseMatrix()
111 :     * man/printSpMatrix.Rd: document, incl. examples
112 :    
113 : maechler 1960 2007-07-04 16:21 Douglas Bates <bates@stat.wisc.edu>
114 :    
115 :     * [r4543] src/cs_utils.c, src/cs_utils.h, src/dgCMatrix.c,
116 :     src/dtCMatrix.c, src/sparseQR.c: CSP typedef for *cs and macro
117 :     AS_CSP. API change - pass the empty structure to Matrix_as_cs.
118 :    
119 : maechler 1945 2007-07-04 Martin Maechler <maechler@stat.math.ethz.ch>
120 :    
121 :     * DESCRIPTION (Version): 0.99875-4
122 :    
123 :     * tests/Class+Meth.R (tstMatrixClass): add dimnames, and hence test
124 :     some dimnames perservation.
125 :    
126 :     * R/dsTMatrix.R (t-method): keep dimnames
127 :     * R/dtTMatrix.R: ditto
128 :    
129 :     * R/sparseMatrix.R (prSpMatrix): print colnames when non-trivial
130 :     and ncol(.) < 10
131 :    
132 :     * src/cs_utils.c: drop check_class() and use Matrix_check_class()
133 :     from Mutils.h
134 :    
135 :     * src/lgCMatrix.c ([ln]csc_to_matrix): no longer lose dimnames,
136 :     e.g. in as(<ngCMatrix>, "matrix")
137 :    
138 : maechler 1960 2007-07-01 13:27 Douglas Bates <bates@stat.wisc.edu>
139 :    
140 :     * [r4529] .: Create a branch for the API changes from the 0.99875
141 :     series to the 0.999375 series
142 :     * [r4530] DESCRIPTION, inst/include/Matrix.h,
143 :     inst/include/Matrix_stubs.c, src/CHMfactor.c, src/Csparse.c,
144 :     src/Mutils.h, src/Tsparse.c, src/chm_common.c, src/chm_common.h,
145 :     src/dense.c, src/dgCMatrix.c, src/dsCMatrix.c, src/dtTMatrix.c,
146 :     src/t_gCMatrix_colSums.c: API change - pass the empty structure to the
147 :     as_cholmod_x functions
148 :    
149 :     2007-06-30 09:05 Martin Maechler <maechler@stat.math.ethz.ch>
150 :    
151 :     * [r4527] trunk/Matrix/DESCRIPTION, trunk/Matrix/NAMESPACE,
152 :     trunk/Matrix/inst/doc/Comparisons.Rnw: add session- and hardware-info
153 :     to Comparisons
154 :    
155 :     >>>>>>> .merge-right.r4561
156 : maechler 1932 2007-06-29 Martin Maechler <maechler@stat.math.ethz.ch>
157 :    
158 :     * DESCRIPTION (Version): 0.99875-3 ready to be released.
159 :    
160 :     * R/sparseMatrix.R (spMatrix): make spMatrix(3,4) working
161 :    
162 :     * R/AllGeneric.R: set "Math" (and "Math2") group generics in a way
163 :     that should also work in a future version of R.
164 :    
165 : maechler 1922 2007-06-21 Martin Maechler <maechler@stat.math.ethz.ch>
166 :    
167 :     * NAMESPACE, R/AllClass.R: "xsparseVector" class union.
168 :    
169 :     * R/sparseVector.R: more *sparseVector coercions, notably for
170 :     non - double ones.
171 :    
172 : maechler 1911 2007-06-19 Martin Maechler <maechler@stat.math.ethz.ch>
173 :    
174 :     * R/colSums.R: new file for all (col|row)(Sums|Means) methods,
175 :     notably the new ones building on the new .Call(.)s:
176 :    
177 :     * src/dgCMatrix.c (DEF_gCMatrix_COLSUMS): use to define
178 :     all 4 of [dlin]gCMatrix_colSums().
179 :    
180 : bates 1909 2007-06-18 16:12 Douglas Bates <bates@stat.wisc.edu>
181 :    
182 :     * [r4472] src/Syms.h, src/init.c: Added Matrix_lengthSym
183 :     * [r4473] src/dgCMatrix.c: Modified dgCMatrix_colSums for sparseVector
184 :     result
185 : maechler 1911
186 : maechler 1903 2007-06-16 Martin Maechler <maechler@stat.math.ethz.ch>
187 :    
188 : maechler 1904 * R/kronecker.R: fix typo (could lead to inf.recursion)
189 :     * test/simple.R: testing that
190 :    
191 : maechler 1903 * R/sparseMatrix.R (prSpMatrix): change to be used as print()
192 : maechler 1922 method as well (which can have arguments, show() can't).
193 : maechler 1903
194 : bates 1902 2007-06-16 15:52 Douglas Bates <bates@stat.wisc.edu>
195 :    
196 :     * [r4466] R/dgCMatrix.R, src/dgCMatrix.c, src/dgCMatrix.h, src/init.c:
197 :     added dgCMatrix_colSums for [col,row][Sums,Means]
198 :    
199 : bates 1899 2007-06-15 23:15 Douglas Bates <bates@stat.wisc.edu>
200 : bates 1897
201 :     * [r4460] R/sparseMatrix.R, man/dgCMatrix-class.Rd, src/dgCMatrix.c,
202 :     src/dgCMatrix.h, src/init.c: added lm.fit.sparse (unexported),
203 :     coercion of "factor" to "dgCMatrix" and dgCMatrix_cholsol
204 :     * [r4461] R/AllClass.R, man/sparseMatrix-class.Rd: draft "indicators"
205 :     class
206 : bates 1899 * [r4463] R/sparseMatrix.R, man/dgCMatrix-class.Rd,
207 :     man/sparseMatrix-class.Rd: Don't need an "indicators" class - use the
208 :     row names to store the levels - duh! Added an example.
209 : maechler 1903
210 : maechler 1893 2007-06-14 Martin Maechler <maechler@stat.math.ethz.ch>
211 :    
212 :     * src/Csparse.c (Csparse_validate): check for *repeated* entries
213 :     thanks to example from Christian Buchta; with a test here:
214 :     * tests/simple.R:
215 :    
216 : maechler 1886 2007-06-07 Martin Maechler <maechler@stat.math.ethz.ch>
217 :    
218 :     * R/Auxiliaries.R (callGeneric): another fix, needed for some cases
219 :     of colSums(*, sparseResult = TRUE)
220 :    
221 : maechler 1883 2007-06-06 Martin Maechler <maechler@stat.math.ethz.ch>
222 :    
223 :     * R/lsparseMatrix.R, R/ldenseMatrix.R (all, any): change default to
224 :     'na.rm = FALSE' as "everywhere" else in R.
225 :    
226 : bates 1877 2007-06-05 Douglas Bates <bates@stat.wisc.edu>
227 :    
228 : bates 1878 * [r4421] src/CSparse_install.sh: Modify for new organization of
229 : maechler 1883 CSparse package
230 : bates 1877 * [r4425] src/UFsparse_download.sh: Update to version 3.0.0 of
231 :     SuiteSparse
232 :     * [r4426] src/Makefile: add ./UFconfig to the include path for
233 :     compilation
234 : maechler 1883 * [r4427] src/cs.[ch]: update to CSparse version 2.2.0
235 :     * [r4428] inst/doc/UFsparse/* src/{AMD,CHOLMOD,COLAMD}/*
236 :     src/UFconfig/UFconfig.h: Update to version 3.0.0 of SuiteSparse
237 :    
238 : maechler 1870 2007-06-05 Martin Maechler <maechler@stat.math.ethz.ch>
239 :    
240 :     * R/Auxiliaries.R (emptyColnames): + argument msg.if.not.empty, used in
241 :     * R/sparseMatrix.R (prSpMatrix): now gives a message about
242 :     suppressed column names.
243 :    
244 : bates 1868 2007-06-04 17:13 Douglas Bates <bates@stat.wisc.edu>
245 :    
246 :     * [r4418] src/Csparse.c, src/HBMM.c, src/Mutils.c, src/Mutils.h,
247 :     src/Tsparse.c, src/chm_common.c, src/chm_common.h, src/dgCMatrix.c,
248 :     src/dgeMatrix.c, src/dpoMatrix.c, src/dpoMatrix.h, src/dppMatrix.c,
249 :     src/dppMatrix.h, src/dsCMatrix.c, src/dspMatrix.c, src/dspMatrix.h,
250 :     src/dsyMatrix.c, src/dsyMatrix.h, src/dtpMatrix.c, src/dtrMatrix.c:
251 :     Remove warnings after change to const char* CHAR
252 :    
253 :     2007-06-04 17:11 Douglas Bates <bates@stat.wisc.edu>
254 :    
255 :     * [r4417] inst/include/Matrix_stubs.c, inst/include/cholmod.h: Corrected
256 :     type of M_cholmod_ssmult
257 :    
258 : bates 1863 2007-06-03 14:42 Douglas Bates <bates@stat.wisc.edu>
259 :    
260 :     * [r4412] inst/include/Matrix_stubs.c, inst/include/cholmod.h,
261 :     src/init.c: Yet another cholmod export - cholmod_ssmult
262 :    
263 : maechler 1855 2007-05-23 Martin Maechler <maechler@stat.math.ethz.ch>
264 :    
265 :     * NAMESPACE: exported drop0(), since
266 :     * man/drop0.Rd: I have seen several cases, I really wanted to use
267 :     it, so our users may want too.
268 :    
269 :     2007-05-22 Martin Maechler <maechler@stat.math.ethz.ch>
270 :    
271 :     * man/colSums.Rd: separately document colSums() etc, since these
272 :     have the extra argument 'sparseResult'.
273 :    
274 : maechler 1852 2007-05-21 Martin Maechler <maechler@stat.math.ethz.ch>
275 :    
276 :     * R/sparseMatrix.R (spMatrix): utility (T)sparse Matrix constructor;
277 :     * man/spMatrix.Rd: docu., including examples
278 :    
279 :     * R/Auxiliaries.R (sp.colMeans): etc, using a patched callGeneric(),
280 :     in order to make colMeans() etc fast *and* correct.
281 :     * R/sparseVector.R (replSPvec): "[<-" functionality for
282 :     sparseVectors; tested in
283 :     * tests/simple.R:
284 :    
285 :     2007-05-19 Martin Maechler <maechler@stat.math.ethz.ch>
286 :    
287 :     * R/sparseMatrix.R (print.sparseSummary): and summary() method for
288 :     (very) sparse Matrices; output similar to Matlab's print().
289 :    
290 : bates 1847 2007-05-17 Douglas Bates <bates@stat.wisc.edu>
291 :    
292 :     * src/HBMM.c (Matrix_writeMatrixMarket): Write 1-based, not
293 :     0-based, indices (Jose Quesada <quesada@gmail.com>).
294 :    
295 : bates 1844 2007-05-16 Douglas Bates <bates@stat.wisc.edu>
296 :    
297 :     * R/CHMfactor.R: Added solve methods for a CHMfactor object.
298 :    
299 : maechler 1845 2007-05-16 Martin Maechler <maechler@stat.math.ethz.ch>
300 :    
301 :     * R/Auxiliaries.R (sparsapply): new utility, much faster than
302 :     tapply1() for large sparse matrices.
303 :    
304 :     2007-05-15 Martin Maechler <maechler@stat.math.ethz.ch>
305 :    
306 :     * R/Matrix.R (dim<-): reshape now via sparseVector.
307 :    
308 :     * R/sparseVector.R: methods and function for
309 :     * R/AllClass.R: new "sparseVector" class and daughters.
310 :     * NAMESPACE: export new classes
311 :    
312 : maechler 1837 2007-05-14 Martin Maechler <maechler@stat.math.ethz.ch>
313 :    
314 :     * DESCRIPTION (Version): 0.99875-1
315 :     * src/Makefile.win: also remove Lapack code from here (cf. 04-25).
316 :    
317 : maechler 1834 2007-05-11 Martin Maechler <maechler@stat.math.ethz.ch>
318 :    
319 :     * R/Tsparse.R ([, Tsparse): fix last case: *duplicated*, symmetric
320 :     indexing
321 :     * tests/indexing.R: test set for that.
322 :    
323 : maechler 1833 2007-05-08 Martin Maechler <maechler@stat.math.ethz.ch>
324 :    
325 :     * R/Tsparse.R (replTmat): fix the case of *duplicated* index
326 :     entries.
327 :     * tests/indexing.R(out): add regression test for it
328 :    
329 :     2007-04-30 Martin Maechler <maechler@stat.math.ethz.ch>
330 :    
331 :     * R/(l(dense|sparse))?Matrix.R (!): use 'x', not 'e1' as argument
332 :     name for "!" method definitions.
333 :    
334 : maechler 1829 2007-04-26 Martin Maechler <maechler@stat.math.ethz.ch>
335 :    
336 :     * R/Tsparse.R (intI): new utility, used for "[" :
337 :     Cleanup up there, and fixes for duplicated indices - more TODO!
338 :    
339 :     * tests/indexing.R(out): more tests
340 :    
341 : bates 1827 2007-04-25 Douglas Bates <bates@stat.wisc.edu>
342 :    
343 :     * DESCRIPTION,src/Makefile: require R>= 2.5.0 and remove Lapack
344 :     code that is now part of the R Lapack library.
345 : maechler 1829
346 : bates 1827 * src/init.c,inst/include/{Matrix_stubs.c,cholmod.h}:export
347 :     cholmod_factorize_p (used in lme4 for GLMMs and NLMMs).
348 :    
349 : maechler 1829 2007-04-21 Martin Maechler <maechler@stat.math.ethz.ch>
350 :    
351 :     * R/Matrix.R (image): method for all Matrices, not just sparse ones.
352 :    
353 :     2007-04-17 Martin Maechler <maechler@stat.math.ethz.ch>
354 :    
355 :     * R/Auxiliaries.R (tapply1): unname(.) -> colSums() etc don't end
356 :     up with extraneous names '0'...'<n-1>'
357 :    
358 : maechler 1825 2007-04-12 Martin Maechler <maechler@stat.math.ethz.ch>
359 :    
360 :     * R/dgTMatrix.R (mat2dgT): care about NAs
361 :    
362 :     2007-04-11 Martin Maechler <maechler@stat.math.ethz.ch>
363 :    
364 :     * R/kronecker.R: triangularity preserving methods
365 :    
366 : maechler 1803 2007-03-27 Martin Maechler <maechler@stat.math.ethz.ch>
367 :    
368 :     * R/kronecker.R: new file collecting kronecker() methods in one
369 :     place. Goal: become much faster!
370 :    
371 : maechler 1799 2007-03-23 Martin Maechler <maechler@stat.math.ethz.ch>
372 :    
373 :     * src/dtCMatrix.c (dtCMatrix_solve): use the new code from Kasper
374 :     Kristensen based cs_spsolve() instead of _lsolve & _usolve which
375 :     can be much faster.
376 :    
377 :     * tests/matprod.R: add regression tests for these (upper & lower).
378 :    
379 :     2007-03-19 Martin Maechler <maechler@stat.math.ethz.ch>
380 :    
381 :     * R/Matrix.R (diff): method for our Matrices.
382 :    
383 :     * R/sparseMatrix.R (isDiagonal): check dim()!
384 :    
385 :     2007-03-17 Martin Maechler <maechler@stat.math.ethz.ch>
386 :    
387 :     * R/Matrix.R (dim<-): new method for "reshape()" built on a
388 :     proposal from Tamas Papp.
389 :    
390 :     2007-03-16 Martin Maechler <maechler@stat.math.ethz.ch>
391 :    
392 :     * R/AllGeneric.R: remove all if(!isGeneric(.)) clauses
393 :    
394 :     * R/zzz.R (.onLoad, .onUnload): do *not* leave bind_activation(TRUE);
395 : maechler 1803 rather define and export cBind() and rBind() only.
396 :     --> useRs *must* change code that used to have cbind()/rbind() !!
397 : maechler 1799
398 : maechler 1803 * R/bind.R: change tests from cbind() to cBind() and similarly to rBind()
399 :     * R/bind.Rout.save: ditto
400 : maechler 1799
401 : bates 1787 2007-02-16 Douglas Bates <bates@r-project.org>
402 :    
403 :     * DESCRIPTION (Date, Version): 0.9975-11 with new date
404 :     * src/dgCMatrix.c (R_to_CMatrix, compressed_to_TMatrix): remove
405 :     const modifier on declaration of the array 'valid'
406 :    
407 : bates 1786 2007-02-12 Douglas Bates <bates@stat.wisc.edu>
408 :    
409 :     * R/CHMfactor.R: Add image method (coercion to sparseMatrix).
410 :    
411 : maechler 1765 2007-02-05 Martin Maechler <maechler@stat.math.ethz.ch>
412 :    
413 : maechler 1768 * DESCRIPTION (Date, Version): 0.9975-10 with new date.
414 :    
415 : maechler 1767 * R/Ops.R (Arith): make sure Csparse o Csparse also works for e.g. ntCMatrix
416 :     * tests/simple.R: test the above and some of these coercions:
417 :    
418 :     * R/nsparseMatrix.R: coercing "Csparse" to "lsparseMatrix";
419 :     be careful to avoid infinite recursion, using new coercions in
420 :     * R/ngCMatrix.R and nsC... and ntC...
421 :     * R/lsparseMatrix.R: ditto
422 :    
423 : maechler 1765 * R/SparseM-conv.R: more conversion, notably for triplet matrices.
424 :    
425 : maechler 1767 * src/dgCMatrix.c (R_to_C_Matrix): port Doug's fix and
426 :     * R/Rsparse.R: reactivate .Call()s
427 : maechler 1765
428 : maechler 1767 * tests/Class+Meth.R: a bit more on actual classes
429 :    
430 :     2007-02-04 Douglas Bates <bates@stat.wisc.edu>
431 :    
432 :     * src/dgCMatrix.c (compressed_to_TMatrix): fix memory bug using strdup()
433 :    
434 : maechler 1760 2007-02-03 Martin Maechler <maechler@stat.math.ethz.ch>
435 : maechler 1758
436 :     * DESCRIPTION (Version): 0.9975-10 to upload
437 :    
438 : maechler 1760 * tests/Class+Meth.R (tstMatrixClass): require coercions to
439 :     specific classes less unconditionally.
440 :    
441 :     * R/Auxiliaries.R: get rid of as_Tsparse() and as_Rsparse()
442 :    
443 :     * R/Tsparse.R (triu): etc, use as(*, "TsparseMatrix") instead of as_Tsparse()
444 :    
445 :     * R/Rsparse.R (.R.2.T): R-level workaround using compressed_to_TMatrix.
446 : maechler 1758 * R/Rsparse.R (.R.2.C): R-level workaround since C-level
447 :     R_to_CMatrix segfaults on one platform.
448 : maechler 1760 Eliminate most coercion method to *specific* classes, and replace
449 :     with virtual classes coercions.
450 : maechler 1758
451 : maechler 1760
452 : maechler 1758 2007-02-01 Martin Maechler <maechler@stat.math.ethz.ch>
453 :    
454 :     * src/init.c: export the CHM...._validate() placeholders, since
455 :     they *are* called.
456 :    
457 : maechler 1760 * tests/Class+Meth.R (classCanCoerce): and starting to test
458 : maechler 1758 all as(<from>, <to>)
459 :    
460 : maechler 1751 2007-01-30 Martin Maechler <maechler@stat.math.ethz.ch>
461 :    
462 :     * R/Tsparse.R ([): more care when subsetting triangular Tsparse
463 :     * tests/indexing.R: tested now
464 :     * tests/indexing.Rout.save: updated
465 :    
466 :     * src/Csparse.c (Csparse_to_dense): use Rkind = -1 for PATTERN to
467 :     * src/chm_common.c (chm_dense_to_SEXP): return "ngeMatrix" when
468 :     appropriate.
469 :    
470 :     * NAMESPACE: export a trivial
471 :     * R/Matrix.R: drop() Matrix-method
472 :    
473 :     * R/AllClass.R: moved all prototypes to virtual super classes.
474 :    
475 :     * R/Rsparse.R: many more coercions to have less exceptions in
476 :     * tests/Class+Meth.R:
477 :    
478 :     * R/Ops.R (Compare): tweak for case with NA
479 :     * tests/simpl.R: hence another 'FIXME' eliminated
480 :    
481 : maechler 1747 2007-01-29 Martin Maechler <maechler@stat.math.ethz.ch>
482 :    
483 : maechler 1748 * R/diagMatrix.R (solve): the obvious methods for diagonalMatrix
484 :     objects.
485 :    
486 : maechler 1747 * tests/Class+Meth.R (tstMatrixClass): now testing diag(), nnzero(),
487 :     and more of "!", "&", "|", all, any; coercions
488 :    
489 :     * R/Rsparse.R: many coercions (which enable quite a few other
490 :     methods), thanks to enhancements in
491 :     * src/dgCMatrix.c (R_to_CMatrix): new, and
492 :     * src/dgCMatrix.c (compressed_to_TMatrix): now for (d,l,n) ,
493 :     symmetric & triangular and ..RMatrix objects.
494 :    
495 :     * src/TMatrix_as.c (Matrix_T_as_DENSE,Matrix_T_as_GENERAL):
496 :     renamed file from src/dsTMatrix.c;
497 :     now dealing with symmetric and triangular Tsparse coercions, both
498 :     to dense and general.
499 :    
500 :     2007-01-27 Martin Maechler <maechler@stat.math.ethz.ch>
501 :    
502 :     * src/dsTMatrix.c: has now "l" and "n" methods besides the "d" ones.
503 :    
504 :     * R/Ops.R (Arith): <dgCMatrix> o <numeric> now remains sparse
505 :     where sensible when the <numeric> is of length > 1.
506 :    
507 :     2007-01-26 Martin Maechler <maechler@stat.math.ethz.ch>
508 :    
509 :     * R/Matrix.R ([<-): for M[] <- value: fix length
510 :    
511 :     2007-01-25 Martin Maechler <maechler@stat.math.ethz.ch>
512 :    
513 :     * R/Auxiliaries.R (n2l_Matrix): new, to be used in
514 :     * R/ndenseMatrix.R: new coercions n* -> l*
515 :    
516 : maechler 1738 2007-01-22 Martin Maechler <maechler@stat.math.ethz.ch>
517 :    
518 :     * R/triangularMatrix.R: new file; simple triu() and tril() methods.
519 :    
520 :     * R/Ops.R ("Logic"): and other "Ops", many updates
521 :    
522 :     2007-01-18 Martin Maechler <maechler@stat.math.ethz.ch>
523 :    
524 :     * src/Mutils.h (SET_DimNames): new utility
525 :    
526 :     * R/Auxiliaries.R (nnzero): improved and now exported via
527 :    
528 :     * NAMESPACE: + nnzero(); length() == prod(dim(.)) method for all "Matrix" objects
529 :    
530 : maechler 1725 2007-01-17 Martin Maechler <maechler@stat.math.ethz.ch>
531 :    
532 :     * R/diagMatrix.R (!): fix typo.
533 :    
534 :     2007-01-16 Martin Maechler <maechler@stat.math.ethz.ch>
535 :    
536 :     * R/Auxiliaries.R (as_Csparse): and quite a few others:
537 :     allow to pass class definition --> speedup
538 :     * R/sparseMatrix.R: apply the above
539 :    
540 :     * R/Csparse.R: coercion Csparse* to dense* now preserves shape properties.
541 :    
542 :     * src/Mutils.h (mMatrix_as_geMatrix): new, based on
543 :     * src/Mutils.c (dup_mMatrix_as_geMatrix): new; generalization of
544 :     old dup_mMatrix_as_dgeMatrix), eliminating a long-standing "FIXME".
545 :    
546 :     * src/dense.c (dense_to_Csparse): use new mMatrix_as_geMatrix()
547 :    
548 :     * R/denseMatrix.R (.dense2C): based on dense_to_Csparse: name it,
549 :     and use it for "sparse*" as well, since it's faster than the
550 :     as_Csparse(.) way.
551 :    
552 :     2007-01-15 Martin Maechler <maechler@stat.math.ethz.ch>
553 :    
554 :     * R/Ops.R ("Logic"): more methods, notably an <lgC> o <lgC> one.
555 :    
556 : maechler 1724 2007-01-12 Martin Maechler <maechler@stat.math.ethz.ch>
557 :    
558 :     * R/Tsparse.R (.TM.repl.i.2col): new internal function to be used
559 :     as method for M[ ij ] <- v
560 :     * R/Csparse.R:: go via Tsparse for "M[ij] <- v"
561 :    
562 :     * R/Ops.R: "Compare" for (C|R)sparse: need pointer slot for all
563 :     FALSE answer
564 :    
565 :     * R/Csparse.R (replCmat): fix the "all non-zero" case with reordering
566 :     * tests/indexing.R: test it, and some of the above
567 :    
568 :     2007-01-05 Martin Maechler <maechler@stat.math.ethz.ch>
569 :    
570 :     * R/Auxiliaries.R (is_duplicatedT): new utility
571 :    
572 : bates 1716 2007-01-05 Douglas Bates <bates@stat.wisc.edu>
573 :    
574 :     * src/init.c (R_init_Matrix): export cholmod_scale
575 :    
576 : maechler 1724 2006-12-30 Martin Maechler <maechler@stat.math.ethz.ch>
577 :    
578 :     * R/zzz.R (tmp): for R >= 2.5.0, extend formals of our
579 :     base::as.matrix to (x, ...)
580 :    
581 : maechler 1714 2006-12-28 Martin Maechler <maechler@stat.math.ethz.ch>
582 :    
583 :     * R/Ops.R ("Arith" etc): move almost all "Ops" methods to new R
584 :     file; start using "Logic", hence
585 :    
586 :     * DESCRIPTION (Depends): R >= 2.4.1 (since we want "Logic")
587 :     * NAMESPACE: import and export "Logic"
588 :    
589 :     2006-12-27 Martin Maechler <maechler@stat.math.ethz.ch>
590 :    
591 :     * src/zpotfr.f and dependencies: use LAPACK 3.1 version
592 :     only needed previously to R version 2.5.0.
593 : maechler 1724
594 : maechler 1710 2006-12-26 Martin Maechler <maechler@stat.math.ethz.ch>
595 :    
596 :     * DESCRIPTION (Date, Version): 0.9975-8, ready for release
597 :    
598 :     * R/Tsparse.R (replTmat): fix subassignment of triangular
599 :     * R/Csparse.R (replCmat): ditto
600 :     * tests/indexing.R: more tests, incl the above fix
601 :    
602 :     2006-12-23 Martin Maechler <maechler@stat.math.ethz.ch>
603 :    
604 :     * R/Auxiliaries.R (drop0): extend for non CSparse
605 :     * R/Auxiliaries.R (diagU2N): should work for all sparseMatrix
606 :    
607 :     * src/Csparse.c (Csparse_to_Tsparse, Csparse_general_to_symmetric):
608 :     use uplo correctly (!); other places: use uplo_P() macro
609 :    
610 :     * R/Csparse.R (replCmat): call diagU2N() when needed
611 :     * R/Tsparse.R (replTmat): ditto
612 :    
613 :     * src/dtCMatrix.c (tCMatrix_validate): new
614 :     * src/dtTMatrix.c (tTMatrix_validate): new, used in
615 :     * R/AllClass.R: for validity of dtC, dsC, and dtT, dsT.
616 :    
617 :     * R/diagMatrix.R (replDiag): to use in [<-
618 :    
619 : maechler 1708 2006-12-22 Martin Maechler <maechler@stat.math.ethz.ch>
620 :    
621 :     * R/Auxiliaries.R (as_Csparse2, as_geSimpl): new functions;
622 :     also more general diagU2N().
623 :    
624 :     2006-12-21 Martin Maechler <maechler@stat.math.ethz.ch>
625 :    
626 :     * R/bind2.R: new file for all cbind2(), rbind() methods moved here
627 :     from R/<foo>Matrix.R files. Better diagonal & improved sparse methods.
628 :    
629 : maechler 1707 2006-12-20 Martin Maechler <maechler@stat.math.ethz.ch>
630 :    
631 :     * tests/bind.R: a few more cases
632 :     * R/Auxiliaries.R (.M.kind): also work for atomic vectors
633 :    
634 :     * R/denseMatrix.R (cbind2/rbind2): moved here (and generalized) from
635 :     * R/ddenseMatrix.R (cbind2/rbind2)
636 :     * R/Tsparse.R (replTmat): final(?!) fix for "[<-" ..
637 :     * tests/indexing.R
638 :     * tests/indexing.Rout.save: updated
639 :    
640 :     2006-12-18 Martin Maechler <maechler@stat.math.ethz.ch>
641 :    
642 :     * R/Tsparse.R (replTmat): fixed a remaining "[<-" bug in
643 :     * tests/indexing.R
644 :    
645 : maechler 1705 2006-12-15 Martin Maechler <maechler@stat.math.ethz.ch>
646 :    
647 :     * R/sparseMatrix.R (prSpMatrix): "." alignment much improved:
648 :     align with proper position of "0", i.e., right for integers.
649 :     argument 'align' by default is "fancy".
650 :    
651 :     2006-12-14 Martin Maechler <maechler@stat.math.ethz.ch>
652 :    
653 :     * R/sparseMatrix.R: delegate "Compare" to "Csparse.."
654 :     * R/Csparse.R: and fix "Compare" for more cases.
655 :     * tests/Class+Meth.R: test some of these (m == m, m != m)
656 :    
657 :     2006-12-13 Martin Maechler <maechler@stat.math.ethz.ch>
658 :    
659 :     * R/lsparseMatrix.R: all() and any() methods
660 :     * R/ldenseMatrix.R: ditto
661 :     * NAMESPACE, R/Matrix.R: ditto
662 :    
663 :     * man/all-methods.Rd: document them minimally
664 :    
665 :     * tests/simple.R: add a few examples for these
666 :    
667 : maechler 1696 2006-12-11 Martin Maechler <maechler@stat.math.ethz.ch>
668 :    
669 :     * R/Tsparse.R ([): fix long standing typo in symmetric case
670 :     * man/dsCMatrix-class.Rd: add example exhibiting the above case
671 :    
672 : bates 1691 2006-12-10 Douglas Bates <bates@stat.wisc.edu>
673 :    
674 :     * src/CHMfactor.c (CHMfactor_to_sparse): change LDL factorization
675 :     to LL before converting to a sparse matrix. (The LDL form can be
676 :     converted to a sparse matrix but it is implicitly a unit
677 :     triangular matrix and a diagonal matrix overwritten on the diagonal.)
678 :    
679 :     2006-12-09 Douglas Bates <bates@stat.wisc.edu>
680 :    
681 :     * src/chm_common.c (chm_factor_to_SEXP): allocate and fill the Dim slot.
682 :    
683 : bates 1688 2006-12-08 Douglas Bates <bates@stat.wisc.edu>
684 :    
685 :     * DESCRIPTION (Version): updated -> release 0.9975-7
686 :     * src/{init.c,chm_common.c}, inst/include/*: export cholmod_analyze_p
687 :    
688 : maechler 1682 2006-11-30 Martin Maechler <maechler@stat.math.ethz.ch>
689 :    
690 :     * R/diagMatrix.R (%*%): write a direct [diag o Csparse] method
691 :    
692 : bates 1681 2006-11-29 Douglas Bates <bates@stat.wisc.edu>
693 :    
694 :     * src/dgeMatrix.c (dgeMatrix_solve): Check error code from dgetri.
695 :     * tests/dg_Matrix.R: Add Barry Rowlingson's test of a matrix that
696 :     is exactly singular.
697 :    
698 : maechler 1674 2006-11-07 Martin Maechler <maechler@stat.math.ethz.ch>
699 :    
700 :     * DESCRIPTION (Date): updated -> release 0.9975-6
701 :    
702 : maechler 1673 2006-11-06 Martin Maechler <maechler@stat.math.ethz.ch>
703 :    
704 :     * R/Csparse.R (replCmat): symmetric indexing of symmetric matrix
705 :     now returns symmetric.
706 :    
707 :     * R/zzz.R ("diag<-"): replace "diag<-" in base for R <= 2.4.x
708 :    
709 :     * R/Matrix.R (.M.sub.i.2col): new, for M[ cbind(i,j) ] indexing.
710 :     * R/Matrix.R (.M.repl.i.2col): new, for M[ cbind(i,j) ] <- value
711 :    
712 :     * R/Auxiliaries.R (.type.kind): added
713 :    
714 :     2006-11-04 Martin Maechler <maechler@stat.math.ethz.ch>
715 :    
716 :     * src/cs.[ch]: updated to CSparse Version 2.0.3 by simply
717 :     running src/CSparse_install.sh
718 :    
719 :     * R/denseMatrix.R: "[": keep symmetric on symmetric indexing.
720 :    
721 : maechler 1665 2006-11-03 Martin Maechler <maechler@stat.math.ethz.ch>
722 :    
723 :     * src/dsCMatrix.c (dsCMatrix_Csparse_solve): new
724 :     * R/dsCMatrix.R (solve): "fully-sparse" using the above.
725 :    
726 :     * R/AllClass.R: "pMatrix" now also inherits from "generalMatrix"
727 :    
728 :     * tests/Class+Meth.R (tstMatrixClass): now assure
729 :     the (important in method programming) property :
730 :    
731 :     ###>> Every "Matrix" is either
732 :     ###>> "general*", "symmetric*", "triangular*" or "diagonal*"
733 :    
734 :     (where "*" stands for "Matrix")
735 :    
736 :     * R/Auxiliaries.R (diagU2N): now .Call()s Csparse_diagU2N for <Csparse>
737 :    
738 :     * R/dMatrix.R (Compare(<dMatrix>,<dMatrix>): update and
739 :     * tests/validObj.R: checks for "comparison"
740 :    
741 :     * R/sparseMatrix.R ([): improved indexing for sparse;
742 :     trying to keep <symmetric>[ n, n] symmmetric
743 :    
744 :     * tests/indexing.R: indexing for logical sparse now ok
745 :    
746 :    
747 : maechler 1660 2006-11-02 Martin Maechler <maechler@stat.math.ethz.ch>
748 :    
749 : maechler 1661 * src/Tsparse.c: use xTsparse_validate() , and hence remove
750 :    
751 :     * src/{ltC,lsC,lgT}Matrix.[ch]: removed
752 :    
753 :     2006-11-02 Martin Maechler <maechler@stat.math.ethz.ch>
754 :    
755 : maechler 1660 * R/AllClass.R (Matrix-class): check length of dimnames in validity.
756 :    
757 :     * tests/simple.R: validObject() checking the above.
758 :    
759 : maechler 1665 * src/dgCMatrix.c (xCMatrix_validate): new, small and simple,
760 : maechler 1660 replacing both dgCMatrix_validate and lgCM*.
761 :    
762 :     * src/Csparse.c (Csparse_dense_prod, etc): do not lose dimnames;
763 :     fix dimnames setting in other places.
764 :     * src/chm_common.c (chm_dense_to_SEXP): now can pass dimnames
765 :    
766 : maechler 1659 2006-11-01 Martin Maechler <maechler@stat.math.ethz.ch>
767 :    
768 : maechler 1660 * R/Csparse.R,src/Csparse.c, etc: tcrossprod(<CsparseM>,<CsparseM>)
769 :    
770 :     * R/sparseMatrix.R (isSymmetric): drop 'factors' slot for
771 :     symmetry test, via
772 : maechler 1659 * R/Auxiliaries.R (.as.dgC.0.factors):
773 :    
774 : bates 1657 2006-11-01 Douglas Bates <bates@r-project.org>
775 :    
776 :     * R/Csparse.R,src/Csparse.c,tests/matprod.R,
777 :     man/CsparseMatrix-class.Rd: crossprod(<CsparseMatrix>,
778 :     <CsparseMatrix>) added
779 :    
780 : maechler 1655 2006-10-30 Martin Maechler <maechler@stat.math.ethz.ch>
781 :    
782 :     * tests/matprod.R: add a variation of Harri's example
783 :    
784 :     * R/dsparseMatrix.R: fix crossprod(<dsparse>, <dge>) to *not*
785 :     recursive infinitely.
786 :    
787 :     * R/dgCMatrix.R: + solve(<sparse>, <sparse>)
788 :    
789 :     * tests/indexing.R: add test for the "<" bug fixed 10-27 in R/dMatrix.R
790 :    
791 :     2006-10-28 Martin Maechler <maechler@stat.math.ethz.ch>
792 :    
793 :     * tests/Class+Meth.R (tstMatrixClass): more: use non-trivial
794 :     matrix if possible; test m+m == 2*m; now test dgRMatrix.
795 :     * R/dgRMatrix.R (.to.dgR): a few more coercions, in order to
796 :     satisfy the above test.
797 :    
798 : maechler 1654 2006-10-27 Martin Maechler <maechler@stat.math.ethz.ch>
799 :    
800 : maechler 1655 * R/Matrix.R (Ops): <Matrix> o <matrix> method added
801 :    
802 : maechler 1654 * R/dgCMatrix.R: solve(a, b="missing") based on
803 :     * src/dgCMatrix.c (dgCMatrix_matrix_solve): extend to work with
804 :     RHS = NULL.
805 :    
806 :     * R/diagMatrix.R (diagdiagprod): extend %*% etc to ldiMatrix;
807 :     add more (needed) [t]crossprod() methods.
808 :    
809 :     * man/ddiMatrix-class.Rd: more info, notably on 'diag'
810 :    
811 :     * R/Auxiliaries.R (as_CspClass): cleanup
812 :     (drop0): internal utility for "Csparse_drop(*, 0)"
813 :     (.bail.out.2): encourage active feedback
814 :    
815 :     2006-10-26 Martin Maechler <maechler@stat.math.ethz.ch>
816 :    
817 :     * R/dMatrix.R(Compare): new(), then slots [no validity check]
818 :    
819 :     * src/Csparse.c (Csparse_validate): fixed (and more efficient in
820 :     non-valid or 'sorted' case).
821 :    
822 :     * R/dsparseMatrix.R: add "chol" method.
823 :     * R/ddenseMatrix.R: ditto
824 :    
825 :     * R/diagMatrix.R (Ops): group methods for <diagonal> o <sparse>
826 :     * NAMESPACE (Ops)
827 :     * R/diagMatrix.R (diag2T): simple utility used "higher level"
828 :     coercion; deprecating direct lower level coercions.
829 :    
830 :     * R/*.R (seq): use seq_len() and seq_along() where possible.
831 :    
832 :    
833 : maechler 1647 2006-10-23 Martin Maechler <maechler@stat.math.ethz.ch>
834 :    
835 :     * DESCRIPTION (Version): 0.9975-5 ready for release
836 :    
837 : bates 1646 2006-10-20 Douglas Bates <bates@stat.wisc.edu>
838 :    
839 :     * src/init.c (R_init_Matrix): export more cholmod CCallable functions.
840 :    
841 : maechler 1642 2006-10-20 Martin Maechler <maechler@stat.math.ethz.ch>
842 :    
843 :     * R/AllClass.R (corMatrix): add 'validity' check;
844 :     comment out unused "LDL" class definition
845 :     * NAMESPACE: mention, but do not export "LDL" class
846 :     * R/corMatrix.R: new (simple), needed for R-devel with
847 :     * tests/Class+Meth.R (tstMatrixClass): 1 exception for corMatrix
848 :     coerce and t() exceptions for all 5 'Mat.MatFact' classes.
849 :    
850 : bates 1641 2006-10-19 Douglas Bates <bates@stat.wisc.edu>
851 :    
852 :     * src/chm_common.h: Add R_cholmod_start to initialize cholmod to
853 :     use Rprintf and R's error handling.
854 :    
855 : maechler 1635 2006-10-17 Martin Maechler <maechler@stat.math.ethz.ch>
856 :    
857 :     * R/diagMatrix.R (%*%): rep(*, each = .) in Matrix %*% diagonal.
858 :     * tests/matprod.R: add tests for the bug fixed.
859 :    
860 : bates 1624 2006-10-11 Douglas Bates <bates@stat.wisc.edu>
861 :    
862 :     * src/HBMM.[ch]: remove HarwellBoeing format for writing.
863 :     * src/SOURCES_C.mkf (SOURCES_C): no longer compile iohb.c
864 :    
865 :     2006-10-06 Douglas Bates <bates@stat.wisc.edu>
866 :    
867 : bates 1629 * R/d[gs]CMatrix.R: deprecate the writeHB function. Use writeMM instead.
868 : bates 1624
869 : maechler 1618 2006-10-06 Martin Maechler <maechler@stat.math.ethz.ch>
870 :    
871 :     * DESCRIPTION (Version): 0.9975-3
872 :    
873 :     * R/diagMatrix.R (bdiag): new function constructing block diagonal
874 :     (sparse) matrices.
875 :     * man/bdiag.Rd: docu + examples
876 :    
877 : maechler 1619 * R/Csparse.R (replCmat): calling new Csparse_drop() now.
878 :    
879 : maechler 1618 * src/Csparse.c (Csparse_general_to_symmetric, Csparse_drop): new functions
880 :     * R/lsCMatrix.R: three more coercions to lsC (thanks to the above)
881 :    
882 :     * R/diagMatrix.R (Diagonal): '[<-' method for diag.matrices such
883 :     that result is sparse or diagonal (and not dense).
884 :    
885 :     * man/Subassign-methods.Rd: fix examples
886 :    
887 :     * R/Matrix.R (Matrix): Matrix(0, *) or Matrix(*, sparse=TRUE)
888 :     should always return a sparse (and not sometimes a diagonal) matrix.
889 :    
890 : maechler 1615 2006-10-05 Martin Maechler <maechler@stat.math.ethz.ch>
891 :    
892 :     * R/Matrix.R ([<-): also for value "Matrix" or "matrix"
893 :    
894 : bates 1613 2006-10-04 Douglas Bates <bates@stat.wisc.edu>
895 :    
896 :     * DESCRIPTION (Version): 0.9975-2
897 : maechler 1615
898 : bates 1613 * inst/include/Matrix_stubs.c (M_cholmod_sparse_to_triplet): export more symbols
899 :    
900 : bates 1611 2006-10-02 Douglas Bates <bates@R-project.org>
901 :    
902 :     * tests/dg_Matrix.R: Simplify test taking into account new code.
903 :    
904 : maechler 1599 2006-09-29 Martin Maechler <maechler@stat.math.ethz.ch>
905 :    
906 : maechler 1600 * R/Csparse.R (replCmat): improve for missing i / j in non-simple cases
907 :    
908 : maechler 1599 * R/lsTMatrix.R: new files w/ missing methods
909 :     * R/nsTMatrix.R: " 'for completeness'
910 :    
911 :     * tests/Class+Meth.R: a bit less 'not.ok.classes'
912 :    
913 :     * R/Tsparse.R (t): generalized "t" method from "dgT*" to "Tsparse*"
914 :    
915 :    
916 : bates 1595 2006-09-28 Douglas Bates <bates@R-project.org>
917 :    
918 :     * src/dppMatrix.h: Ensure definition of dspMatrix_validate is
919 :     included.
920 :    
921 :     * src/init.c, inst/include/{Matrix.h,Matrix_stubs.h,cholmod.h}:
922 :     Export C-callable functions used in Zt_create in lme4.
923 :    
924 : maechler 1592 2006-09-28 Martin Maechler <maechler@stat.math.ethz.ch>
925 :    
926 :     * DESCRIPTION (Version): 0.9975-1
927 :    
928 :     * tests/simple.R: less checks fail; using NA, found that our
929 :     kronecker() is not base-compatible with NA's.
930 :    
931 :     * R/dMatrix.R: "Compare" method now implemented for all cases
932 :    
933 :     * R/Auxiliaries.R (indTri): == which([lower/upper].tri( * )) new utility
934 :    
935 :     * man/dtpMatrix-class.Rd: mention length of 'x' slot
936 :    
937 :     * src/dtpMatrix.c (dtpMatrix_validate): fix check
938 :     * src/dspMatrix.c (dspMatrix_validate): ditto
939 :    
940 :     * R/dtTMatrix.R (gt2tT): fix ("l" -> "n")
941 :     including coercion to [nl]tTMatrix.
942 :    
943 :     * R/diagMatrix.R (show): print a header line as for other classes.
944 :    
945 :     2006-09-27 Martin Maechler <maechler@stat.math.ethz.ch>
946 :    
947 :     * src/Makefile.win (SUBDIRS): fix typo
948 :    
949 : maechler 1583 2006-09-19 Martin Maechler <maechler@stat.math.ethz.ch>
950 :    
951 :     * DESCRIPTION (Date): ready to release 0.9975-0 to CRAN
952 :    
953 : bates 1577 2006-09-18 Douglas Bates <bates@stat.wisc.edu>
954 :    
955 :     * R/[CT]sparse.R (crossprod and tcrossprod): Handle the cases for x
956 :     symmetric and y missing in R code using %*% (cholmod_aat doesn't
957 :     accept a symmetric matrix).
958 :     * tests/group-methods.R: Uncomment test of crossprod applied to
959 :     lsCMatrix objects.
960 :    
961 : maechler 1575 2006-09-18 Martin Maechler <maechler@stat.math.ethz.ch>
962 :    
963 :     * R/AllClass.R (symmetricMatrix): add validity method (available
964 :     in C for a long time). Many "n..Matrix": drop (wrong) validity arg.
965 :    
966 :     * src/lgCMatrix.c (lgCMatrix_validate): check 'x' slot (!)
967 :    
968 :     * tests/indexing.Rout.save:
969 :     * tests/indexing.R: additions, mainly for 'lsparse'
970 :    
971 :     * R/diagMatrix.R (Diagonal) & coercion to lgTMatrix: fixes for NA
972 :     case.
973 :    
974 :     * R/Auxiliaries.R (nz.NA): new utility now used in nnzero()
975 :    
976 : maechler 1571 2006-09-16 Martin Maechler <maechler@stat.math.ethz.ch>
977 :    
978 : maechler 1572 * R/sparseMatrix.R (prSpMatrix): print logical NAs "visibly"
979 :     as 'N' (1-letter - Ok?)
980 :    
981 : maechler 1571 * tests/group-methods.R: add test for logical + NAs
982 :    
983 :     * R/dMatrix.R ("Compare"): fix to work with NA's
984 :    
985 :     * R/AllClass.R: "Cholesky" etc now inherit from MatrixFactorization.
986 :    
987 :     * src/lgCMatrix.c (ncsc_to_matrix): renamed from lcsc_to_matrix()
988 :     which is implemented.
989 :    
990 : maechler 1565 2006-09-15 Martin Maechler <maechler@stat.math.ethz.ch>
991 :    
992 : maechler 1571 * src/chm_common.c: coerce logical <-> double instead of
993 :     typecasting; needed for "l" matrix handling in cholmod.
994 : maechler 1565
995 : maechler 1571 * tests/other-pkgs.R (graph): small extension in "graph" checks.
996 :    
997 : maechler 1565 * R/sparseMatrix.R (graphNEL -> Tsparse): method for weight case.
998 :     (Tsp2grNEL): other fixes needed
999 :    
1000 : maechler 1548 2006-09-11 Martin Maechler <maechler@stat.math.ethz.ch>
1001 :    
1002 :     * R/AllClass.R ("nMatrix"): and subclasses for "nonzero pattern"
1003 :     Matrices, since "lMatrix", also "lsparseM" can have NA
1004 :     * R/ndenseMatrix.R, etc: new source files
1005 :     * man/nsparseMatrix-classes.Rd, etc: new help files
1006 :     * tests/: adaptions
1007 :     * src/chm_common.c (chm_dense_to_SEXP): and others:
1008 :     new 'Rkind' argument: "l*" and "d*" both use CHOLMOD_REAL
1009 : maechler 1582 * src/Csparse.c, etc: ditto
1010 : maechler 1548
1011 : bates 1546 2006-09-11 Douglas Bates <bates@R-project.org>
1012 :    
1013 :     * src/Mutils.[ch],init.c inst/include/*.h: Move the
1014 :     alloc_d**Matrix functions to the lme4 package.
1015 :    
1016 : bates 1543 2006-09-09 Douglas Bates <bates@R-project.org>
1017 :    
1018 :     * src/dsCMatrix.c (dsCMatrix_Cholesky): igoring LDL = FALSE now
1019 : maechler 1544 fixed
1020 : bates 1543
1021 : maechler 1544 2006-09-09 Martin Maechler <maechler@stat.math.ethz.ch>
1022 :    
1023 : maechler 1548 * R/lMatrix.R: new
1024 :    
1025 : maechler 1544 * R/sparseMatrix.R (Tsp2grNEL): do not yet use graph::foo()
1026 :    
1027 :     * R/dgeMatrix.R: do not define tcrossprod() methods for "matrix"
1028 : maechler 1582 * man/tcrossprod.Rd: ditto
1029 : maechler 1544
1030 : bates 1538 2006-09-08 Douglas Bates <bates@stat.wisc.edu>
1031 :    
1032 :     * inst/include/Matrix_stubs.c,Matrix.h: Add declarations and stubs
1033 :     for exported functions
1034 :     * src/Makefile, src/CHOLMOD/Lib/Makefile, src/Metis,CAMD,CCOLAMD:
1035 :     Remove partitioning algorithms for sparse matrix reordering. The
1036 :     copyright on the Metis code was problematic and the methods were
1037 :     rarely used.
1038 :     * src/triplet_to_col.[ch],MMHB.[ch]: Remove triplet_to_col. Such
1039 :     operations are now done entirely in CHOLMOD code.
1040 :    
1041 : bates 1517 2006-09-06 Douglas Bates <bates@R-project.org>
1042 :    
1043 :     * src/Mutils.h: Remove functions that are no longer used.
1044 :    
1045 : bates 1507 2006-09-04 Douglas Bates <bates@R-project.org>
1046 :    
1047 :     * src/dtCMatrix.c (dtCMatrix_validate): rename functions.
1048 :     * src/DEPS.mkf: update
1049 :    
1050 : maechler 1481 2006-09-02 Martin Maechler <maechler@stat.math.ethz.ch>
1051 :    
1052 :     * created branches/Matrix-for-R-2.3.x; on trunk: do
1053 :     * DESCRIPTION (Version): 0.9975-0
1054 :     (Depends): R (>= 2.4.0)
1055 :    
1056 : bates 1475 2006-09-01 Douglas Bates <bates@R-project.org>
1057 :    
1058 :     * R/sparseMatrix.R: Added direct method to CsparseMatrix from graphNEL
1059 :    
1060 : maechler 1472 2006-09-01 Martin Maechler <maechler@stat.math.ethz.ch>
1061 :    
1062 :     * R/sparseMatrix.R: add coercion from "ANY" to "sparseMatrix"
1063 :     * R/denseMatrix.R: add coercion from "ANY" to "denseMatrix"
1064 :    
1065 :     * R/Matrix.R ([): use nargs() to disambiguate M[i] and M[i,]
1066 :    
1067 :     2006-08-31 Martin Maechler <maechler@stat.math.ethz.ch>
1068 :    
1069 :     * R/sparseMatrix.R (Arith): moved Arith group method one-level up
1070 :     from "dsparse" to "sparse" and now go via "Csparse" instead of "dgC"
1071 : maechler 1582 * R/dsparseMatrix.R: ditto
1072 :     * R/Csparse.R: ditto
1073 : maechler 1472
1074 :     2006-08-31 Martin Maechler <maechler@stat.math.ethz.ch>
1075 :    
1076 :     * R/dMatrix.R (Compare): improve availability of "<", etc
1077 :     * R/Auxiliaries.R (asTuniq): new; also make use of R 2.4.x print(*,max)
1078 :    
1079 : maechler 1467 2006-08-30 Martin Maechler <maechler@stat.math.ethz.ch>
1080 :    
1081 :     * R/dgCMatrix.R: aargh: "Arith(<dgC>, numeric)" was wrong because
1082 :     of a 0-index which was used as 1-index (..hmm)
1083 :    
1084 :     * R/sparseMatrix.R (prSpMatrix): fix printing an all-0 sparse Matrix
1085 :    
1086 :     * R/Auxiliaries.R (all0, is0): for 0-testing in presence of NA's
1087 :     * R/Auxiliaries.R (isTriMat): use all0() for 0-testing.
1088 : maechler 1582 (.is.diagonal): ditto
1089 : maechler 1467
1090 :     * R/lgTMatrix.R: as("matrix", "lgTMatrix"): warn about NA's
1091 :    
1092 :     * R/Matrix.R (Matrix): also work for NA data
1093 :    
1094 : maechler 1455 2006-08-28 Martin Maechler <maechler@stat.math.ethz.ch>
1095 :    
1096 :     * R/Matrix.R (Matrix): + 'forceCheck' argument; dimnames setting
1097 :     in all cases.
1098 :    
1099 : bates 1453 2006-08-27 Douglas Bates <bates@R-project.org>
1100 :    
1101 :     * src/dense.[ch],init.c, R/ddenseMatrix.R, man/band.Rd
1102 :     (ddense_band): Added triu, tril and band for ddenseMatrix objects.
1103 :    
1104 : maechler 1447 2006-08-25 Martin Maechler <maechler@stat.math.ethz.ch>
1105 :    
1106 :     * src/Mutils.c (dup_mMatrix_as_dgeMatrix): added all subclasses of
1107 :     subclasses of "ddenseMatrix"
1108 :     * src/init.c et al: outcomment dtrM*_as_dge* and dsyM*_as_dge*_
1109 :     * R/ddenseMatrix.R et al: setAs("ddenseMatrix", "dgeMatrix", ..)
1110 :     instead of half dozen specialized ones.
1111 :    
1112 : bates 1445 2006-08-25 Douglas Bates <bates@R-project.org>
1113 :    
1114 :     * R/lmer.R (qqmath method): Bug fix provided by Emmanuel Tillard
1115 :     <tillard@cirad.fr> - ordering standard errors to match effects.
1116 :    
1117 : bates 1439 2006-08-24 Douglas Bates <bates@R-project.org>
1118 : bates 1431
1119 : bates 1439 * src/lsCMatrix.c (lsCMatrix_trans): Remove lsCMatrix_chol based
1120 :     on R_ldl.
1121 :     * R/lCholCMatrix.R,
1122 :     src/[dl]CholCMatrix.[ch],R_ldl.[ch],Metis_utils.[ch]: removed
1123 :     * src/dsCMatrix.c (dsCMatrix_to_dgTMatrix): use CHOLMOD
1124 :     * many files in ./R and ./src: Use more general version of
1125 :     dup_mMatrix_as_dgeMatrix to simplify method definitions.
1126 : bates 1442 * src/Mutils.c (dup_mMatrix_as_dgeMatrix): Add ddiMatrix,
1127 :     dtpMatrix, dspMatrix and dppMatrix conversions.
1128 :    
1129 : maechler 1447
1130 : bates 1439 2006-08-23 Douglas Bates <bates@R-project.org>
1131 :    
1132 :     * R/AllClass.R,lCholCMatrix.R,src/SOURCES_C.mkf,init.c,NAMESPACE:
1133 :     Remove classes lCholCMatrix and dCholCMatrix based on R_ldl code.
1134 : bates 1431 * src/dgeMatrix.c: Ensure 'factors' slot exists in result of
1135 :     dgeMatrix_crossprod (may need to do this in other places).
1136 :     * R/AllGeneric.R,dsCMatrix.R, src/dscMatrix.[ch]: Add Cholesky
1137 :     generic and method for dsCMatrix. Use CHOLMOD for chol().
1138 :    
1139 : bates 1414 2006-08-22 Douglas Bates <bates@R-project.org>
1140 :    
1141 :     * src/Mutils.c (dup_mMatrix_as_dgeMatrix): updated for general
1142 :     types of classed Matrices, matrices or numeric or logical vectors.
1143 : bates 1423 * src/init.c: register dup_mMatrix_as_dgeMatrix for coercions.
1144 :     * src/chm_common.c,Mutils.h (as_cholmod_factor): Move check_class
1145 :     to Mutils.h (as an inline) and change name to Matrix_check_class;
1146 :     fixes in as_cholmod_factor and chm_factor_to_SEXP.
1147 :     * src/dsCMatrix.[ch]: Use CHOLMOD for dsCMatrix_chol and
1148 :     dsCMatrix_matrix_solve. Comment out vestigial functions.
1149 :     * src/Csparse.c: use diag_P and uplo_P macros.
1150 : maechler 1447
1151 : bates 1405 2006-08-21 Douglas Bates <bates@R-project.org>
1152 :    
1153 :     * src/lmer.c (internal_mer_RZXinv): Fix memory leak caught by
1154 : maechler 1447 valgrind.
1155 : bates 1411 * tests/matprod.R: Add tests to verify that 'solve' and '%*%' are
1156 :     inverses.
1157 :     * src/sparseQR.c (sparseQR_validate): add new validation test, fix
1158 :     -Wall warnings.
1159 :     * src/dppMatrix.c,dtrMatrix.c,dgCMatrix.c,dgeMatrix.c,dspMatrix.c:
1160 :     Use dup_mMatrix_as_dgeMatrix.
1161 : maechler 1447
1162 : bates 1403 2006-08-20 Douglas Bates <bates@R-project.org>
1163 :    
1164 :     * src/sparseQR.c: Fix thinko in sparseQR_resid_fitted.
1165 :     * tests/sparseQR.R: Added
1166 :     * man/sparseQR-class.Rd: Document methods for qr.* generics
1167 :     * R/sparseQR.R: Return correct # of coefs; fix cut-and-paste errors
1168 :    
1169 : bates 1398 2006-08-19 Douglas Bates <bates@R-project.org>
1170 :    
1171 :     * NAMESPACE, R/sparseQR.R, src/init.c,sparseQR.[ch],SOURCES_C.mkf:
1172 :     Added methods for sparseQR for qr.qy, qr.qty, qr.coef, qr.resid
1173 :     and qr.fitted.
1174 :     * src/Mutils.[ch]: Added dup_mMatrix_as_dgeMatrix utility
1175 :     * src/dgCMatrix.c: Check for ordering before storing q in dgCMatrix_QR
1176 :    
1177 : maechler 1389 2006-08-18 Martin Maechler <maechler@stat.math.ethz.ch>
1178 :    
1179 :     * R/AllGeneric.R: add "qr" and "chol" generics; via 'trick' since
1180 :     the base version has no "..." argument.
1181 :    
1182 :     * R/sparseMatrix.R (prSpMatrix): fix the triangular unit diagonal case.
1183 :    
1184 :     * R/Matrix.R: define and
1185 :     * NAMESPACE: export as.numeric() and as.logical() methods.
1186 :     Let's hope these do not badly slow down something...
1187 :     Finally export the zapsmall() method.
1188 :    
1189 : bates 1388 2006-08-17 Douglas Bates <bates@R-project.org>
1190 :    
1191 :     * src/dgCMatrix.[ch] (dgCMatrix_matrix_solve), src/init.c,
1192 :     R/dgCMatrix.R: solve methods for dgCMatrix and dense RHS.
1193 :     * src/dtCMatrix.c :Remove code that is no longer used
1194 :     * R/dtCMatrix.R: Use C code for diagU2N in CsparseMatrix classes
1195 :    
1196 : bates 1370 2006-08-14 Douglas Bates <bates@R-project.org>
1197 :    
1198 : bates 1373 * src/Csparse.[ch],init.c (Csparse_to_logical): Added utilities
1199 :     Csparse_to_logical and Csparse_symmetric_to_general.
1200 :     * R/dgCMatrix.R,dsCMatrix.R,Csparse.R : Consolidate general
1201 : maechler 1389 coercion methods between CsparseMatrix and TsparseMatrix.
1202 : bates 1373
1203 :     2006-08-14 Douglas Bates <bates@R-project.org>
1204 :    
1205 : bates 1370 * R/dtCMatrix.R,dgCMatrix.R,Csparse.R src/init.c,dgCMatrix.[ch],
1206 :     Csparse.[ch],chm_common.c,dense.c : Use CHOLMOD code and methods
1207 :     for CsparseMatrix, TsparseMatrix, denseMatrix or matrix when
1208 :     possible.
1209 :    
1210 : bates 1368 2006-08-12 Douglas Bates <bates@R-project.org>
1211 :    
1212 :     * src/chm_common.[ch],Csparse.[ch],Tsparse.[ch],CHMfactor.c,dtTMatrix.c,
1213 :     dgTMatrix.c,dgCMatrix.c,dsCMatrix.c,dtTMatrix.c, R/dsTMatrix.R,
1214 :     Tsparse.R,Csparse.R,dgTMatrix.R,dsCMatrix.R,lsCMatrix.R:
1215 :     generalize conversions between TsparseMatrix, CsparseMatrix,
1216 :     denseMatrix and matrix. Preserve triangularity property and
1217 :     propagate Dimnames in the easy cases.
1218 :    
1219 : bates 1365 2006-08-10 Douglas Bates <bates@R-project.org>
1220 :    
1221 :     * src/lmer.c: adjust checks in glmer_init for S4SXP
1222 :     * tests/validObj.R: check of all(eq) should be all(eq@x) - worked
1223 :     before S4SXP but for the wrong reasons.
1224 :    
1225 : bates 1354 2006-08-08 Douglas Bates <bates@R-project.org>
1226 :    
1227 : bates 1360 * src/Csparse.c (Csparse_crossprod): tcrossprod result has stype = -1.
1228 :     Later modified to return the upper triangle only.
1229 :     * R/dgTMatrix.R: Remove vestigial crossprod and tcrossprod methods.
1230 : maechler 1389
1231 : bates 1352 2006-08-07 Douglas Bates <bates@R-project.org>
1232 :    
1233 :     * src/Csparse.c (Csparse_crossprod): Set stype on result to avoid
1234 :     R-level conversion to a sparse symmetric class.
1235 :     * R/Tsparse.R,R/Csparse.R (crossprod and tcrossprod methods):
1236 :     Remove conversion to sparse symmetric classes (now done in C code).
1237 :    
1238 : maechler 1349 2006-08-07 Martin Maechler <maechler@stat.math.ethz.ch>
1239 :    
1240 : maechler 1351 * R/dgCMatrix.R: disable old crossprod and tcrossprod methods
1241 :     * man/band.Rd: adapt the \dontshow{} unit test.
1242 :    
1243 :     2006-08-07 Martin Maechler <maechler@stat.math.ethz.ch>
1244 :    
1245 : maechler 1349 * DESCRIPTION (Version): 0.995-14 for CRAN
1246 :    
1247 :     * tests/other-pkgs.R: oops: library(Matrix) outside *if* !
1248 :    
1249 :     * R/sparseMatrix.R (Tsp2grNEL): fixed Tsparse -> graph coercion
1250 :     * tests/other-pkgs.R: more checks, sparseMatrix -> graph
1251 :    
1252 :     * R/Auxiliaries.R (as_Tsparse, as_Rsparse): new
1253 :     * R/Tsparse.R (tril, triu, band): methods
1254 : bates 1352 * R/dgRMatrix.R (tril, ...): ditto
1255 :     * man/band.Rd: ditto
1256 : maechler 1349
1257 :     2006-08-04 Martin Maechler <maechler@stat.math.ethz.ch>
1258 :    
1259 :     * R/Matrix.R (head, tail): directly use utils:::head.matrix
1260 :     to be up-to-date automatically.
1261 :    
1262 : maechler 1346 2006-08-03 Martin Maechler <maechler@stat.math.ethz.ch>
1263 :    
1264 :     * DESCRIPTION (Version): 0.995-13 to be released to CRAN
1265 :    
1266 :     * DESCRIPTION (Lazydata): no, instead of 'yes' because it fails for:
1267 :     * data/CAex.R, inst/external/CAex_slots.rda: replacing data/CAex.rda
1268 :     * data/KNex.R, inst/external/KNex_slots.rda: replacing data/KNex.rda
1269 :     such that the S4 objects are always created by the current version
1270 :     of R and 'Matrix' class definitions.
1271 :    
1272 : bates 1342 2006-08-01 Douglas Bates <bates@R-project.org>
1273 :    
1274 :     * R/lmer.R (LMEoptimize method), tests/lmer.R,
1275 : maechler 1346 inst/external/test3comp.rda: Added warnings for convergence on
1276 : bates 1342 boundary and test cases.
1277 :    
1278 :     * src/lmer.c (mer_postVar): Modified to return the variances that
1279 :     are marginal to the fixed effects, not conditional on them (which
1280 :     is what the bVar slot contents represent).
1281 :    
1282 : bates 1338 2006-07-31 Douglas Bates <bates@R-project.org>
1283 :    
1284 :     * NAMESPACE, src/lmer.c, R/lmer.R (hatTrace): Add the hatTrace
1285 :     function which calls the C function mer_hat_trace2.
1286 : maechler 1346
1287 : bates 1342 * man/ranef.Rd: Include description of "postVar" argument and
1288 :     producing a caterpillar plot.
1289 : bates 1338
1290 : maechler 1335 2006-07-31 Martin Maechler <maechler@stat.math.ethz.ch>
1291 :    
1292 :     * NAMESPACE: change "correlation" to "corMatrix"
1293 :     * R/AllClass.R: to avoid clash with S3 class in 'nlme'.
1294 : bates 1352 * R/dpoMatrix.R: ditto
1295 :     * R/lmer.R: ditto
1296 : maechler 1335
1297 : bates 1338 2006-07-28 Douglas Bates <bates@R-project.org>
1298 :    
1299 :     * src/lmer.c (internal_mer_RZXinv): Split the calculation of the
1300 :     RZXinv slot's contents into a separate internal function that can
1301 :     be used in mer_hat_trace.
1302 :    
1303 : maechler 1331 2006-07-22 Martin Maechler <maechler@stat.math.ethz.ch>
1304 :    
1305 :     * R/Matrix.R: Coercions "Matrix" -> (sparse|dense)Matrix
1306 :     via new smart
1307 :     * R/Auxiliaries.R (as_Csparse, as_dense, .M.shapse): new
1308 :     utility functions.
1309 :    
1310 :    
1311 : maechler 1330 2006-07-21 Martin Maechler <maechler@stat.math.ethz.ch>
1312 :    
1313 : maechler 1331 * R/Csparse.R (tril, triu, band): do return *triangular* classed
1314 :     matrices when appropriate; band() even symmetric ones.
1315 :     (replCmat): extend to potentially all "CsparseMatrix"
1316 :     * R/Tsparse.R (replTmat): extend to all "TsparseMatrix"; hence
1317 :     allow subassignment for special sparse matrices.
1318 :    
1319 :     * R/Auxiliaries.R (as_geClass): factor out the .M.kind() functionality
1320 :    
1321 : maechler 1330 * src/lmer.c (mer_MCMCsamp, glmer_MCMCsamp): new 'verbose'
1322 :     argument; in glmer_*(): print only if(verbose).
1323 :    
1324 :     speed-optimize a few places by moving REAL(.) out of loops.
1325 :    
1326 :     * src/lmer.h, src/init.h, R/lmer.R: related to above.
1327 :    
1328 : maechler 1329 2006-07-20 Martin Maechler <maechler@stat.math.ethz.ch>
1329 :    
1330 :     * R/Matrix.R("["): disable ("Matrix", i = "logical", j = "missing"),
1331 :     since that wrongly triggers also for M[ logi , ]
1332 :    
1333 :     * R/denseMatrix.R: "[" methods now also work e.g. when indexing
1334 :     a symmetric matrix that results in a non-symmetric one.
1335 :     * R/Auxiliaries.R (as_geClass): new function used in "[" above.
1336 :    
1337 :     * R/dMatrix.R: make round(M) work as round(M, 0)
1338 :    
1339 :     * R/dgTMatrix.R (image): coordinate system and axis now use
1340 :     1-based indices, not 0-based ones.
1341 :    
1342 :     * R/Tsparse.R (.ind.prep for "["): get rid of max(<empty>) warning.
1343 :     * tests/indexing.R: test it.
1344 :    
1345 :     * NAMESPACE: export isSymmetric(); has been a generic in "base" for a while;
1346 :     * man/isSymmetric-methods.Rd: and document it.
1347 :    
1348 :     * R/SparseM-conv.R: added coercion methods for some 'SparseM' matrices.
1349 :     * man/SparseM-conv.Rd: docu them
1350 :    
1351 :     * tests/other-pkgs.R: renamed from tests/graph.R and add example
1352 :     for 'SparseM' conversions
1353 :    
1354 :     2006-07-17 Douglas Bates <Douglas.Bates@R-project.org>
1355 :    
1356 :     * R/Matrix.R (head): added head() and tail() methods.
1357 :    
1358 :     2006-07-17 Martin Maechler <maechler@stat.math.ethz.ch>
1359 :    
1360 :     * DESCRIPTION (Version): 0.995-12 released to CRAN
1361 :    
1362 : maechler 1319 2006-07-15 Martin Maechler <maechler@stat.math.ethz.ch>
1363 :    
1364 :     * tests/simple.R: add check for correct dsT -> dgT coercion;
1365 :     add check for correct printing of symmetric sparse matrices.
1366 :    
1367 :     * R/Auxiliaries.R (non0ind): return *all* non-0 entry indices also
1368 :     for sparse symmetric matrices.
1369 :    
1370 :     * src/dsTMatrix.c (dsTMatrix_as_dgTMatrix): do not copy the
1371 :     diagonal twice.
1372 :    
1373 : bates 1316 2006-07-11 Douglas Bates <Douglas.Bates@R-project.org>
1374 :    
1375 :     * src/dsTMatrix.c (dsTMatrix_as_dgTMatrix): Fix a case of INTEGER
1376 : maechler 1319 being applied to the x slot (detected by Brian Ripley).
1377 : bates 1316
1378 : maechler 1315 2006-07-10 Martin Maechler <maechler@stat.math.ethz.ch>
1379 :    
1380 :     * src/dgCMatrix.c (dgCMatrix_validate): 'p' slot must have correct length.
1381 :    
1382 :     * R/Auxiliaries.R (isTriC): fix buglet (we were 1-based!)
1383 :    
1384 :     2006-07-08 Martin Maechler <maechler@stat.math.ethz.ch>
1385 :    
1386 :     * src/lgCMatrix.c (lgCMatrix_diag): new function
1387 :     * R/lgCMatrix.R (diag): for new method
1388 :    
1389 :     * R/AllClass.R (TsparseMatrix): do use Tsparse_validate
1390 :     ==> construction of illegal "*gTMatrix" via new() should
1391 :     now be much less easy:
1392 :     * tests/Class+Meth.R: assertError() for some illegal "dgT*"
1393 :    
1394 :     * R/Matrix.R (Matrix): Matrix(0, nrow,ncol) now "goes sparse"
1395 :     directly.
1396 :     * man/Matrix.Rd: documents it.
1397 :    
1398 : bates 1311 2006-07-06 Douglas Bates <bates@R-project.org>
1399 :    
1400 :     * src/pedigree.c (pedigree_inbreeding): Correction in
1401 :     initialization. This function is not currently being used and is
1402 :     not fully tested.
1403 :    
1404 : bates 1312 * NAMESPACE, R/{AllClass.R,lmer.R}, src/{init.c,lmer.c}:
1405 :     Introduced the glmer class. Added code for mcmcmsamp on glmer
1406 :     objects. Modified validity check on pedigree objects to account
1407 :     for nonparallel patterns of missingness of parents.
1408 : bates 1311
1409 : bates 1313 * man/{lmer-class.Rd,mcmcsamp.Rd}: Update documentation for glmer
1410 :     class.
1411 : maechler 1315
1412 :     2006-07-01 Martin Maechler <maechler@stat.math.ethz.ch>
1413 :    
1414 :     * R/pMatrix.R: coercion pMatrix -> Tsparse
1415 :    
1416 : bates 1300 2006-06-12 Douglas Bates <bates@R-project.org>
1417 :    
1418 : maechler 1319 * DESCRIPTION (Version): 0.995-11 released to CRAN
1419 :    
1420 : bates 1300 * R/lmer.R (mcmcsamp method): Corrected arrangments of names on
1421 :     the output from mcmcsamp.
1422 :    
1423 : bates 1298 2006-06-10 Douglas Bates <bates@R-project.org>
1424 :    
1425 : bates 1300 * R/lmer.R (simulestimate): added C code for calculating the trace
1426 :     of the hat matrix.
1427 : bates 1298
1428 : maechler 1295 2006-06-09 Martin Maechler <maechler@stat.math.ethz.ch>
1429 :    
1430 :     * R/diagMatrix.R (setAs): define coercion methods to sparse matrix
1431 :     classes.
1432 : maechler 1315 * R/sparseMatrix.R etc: multiplication of diagonal and sparse
1433 : maechler 1295
1434 : maechler 1290 2006-06-08 Martin Maechler <maechler@stat.math.ethz.ch>
1435 :    
1436 :     * R/dgTMatrix.R (colSums): etc. All four of
1437 :     colSums(), rowSums(), colMeans(), rowMeans() now should work for
1438 :     all "Matrices".
1439 :    
1440 : bates 1288 2006-06-01 Douglas Bates <bates@stat.wisc.edu>
1441 :    
1442 :     * R/lmer.R (panel.ci): Add a reference line at zero and a
1443 :     background grid to the qqmath plot of ranef.lmer.
1444 :    
1445 : bates 1287 2006-05-30 Douglas Bates <bates@stat.wisc.edu>
1446 : bates 1284
1447 : bates 1287 * R/lmer.R (expandSlash): Functions (non-exported) to allow nested
1448 :     grouping factors to be specified in the formula as (1|foo/bar).
1449 :    
1450 :     2006-05-27 Douglas Bates <bates@stat.wisc.edu>
1451 :    
1452 : bates 1284 * R/lmer.R (findbars and others): Change check of is.numeric to
1453 :     !is.language to resolve the bug reported by Jacob Wegelin.
1454 :    
1455 :     * src/pedigree.c (pedigree_inbreeding): Initial implementation of
1456 :     code to evaluate inbreeding coefficients without calculating T,
1457 :     based on code in Sargolzaei and Iwaisaki's paper.
1458 :    
1459 : bates 1283 2006-05-27 Douglas Bates <bates@stat.wisc.edu>
1460 :    
1461 :     * R/{lmer.R,AllGeneric.R}, src/{init.c,lmer.[ch]}: Added local
1462 :     generic and mer methods for isNested and denomDF. This denomDF was
1463 :     an attempt to emulate that in lme but I don't think that makes
1464 :     sense. Use the trace of the hat matrix instead.
1465 :    
1466 : maechler 1271 2006-05-17 Martin Maechler <maechler@stat.math.ethz.ch>
1467 :    
1468 :     * R/sparseMatrix.R: Matrix <-> graph methods: can no longer use
1469 :     the C code depending on a slot structure that's no longer valid.
1470 : bates 1352 * src/dgTMatrix.c: ditto (also: src/init.c src/dgTMatrix.h)
1471 : maechler 1271
1472 :    
1473 : bates 1268 2006-05-17 Douglas Bates <bates@stat.wisc.edu>
1474 :    
1475 :     * R/{AllGeneric.R,Csparse.R},man/band.Rd,NAMESPACE: changed name
1476 :     of lowerTriMatrix generic and methods to tril (also upper to triu)
1477 :     and added a general band extractor.
1478 :    
1479 : bates 1267 2006-05-16 Douglas Bates <bates@stat.wisc.edu>
1480 :    
1481 :     * R/pedigree.R (pedigree): Replace sire and dam values outside the
1482 :     allowable range with NAs. Added a corresponding check in the
1483 :     validity check for the pedigree class.
1484 :    
1485 :     * R/[CT]sparse.R ([t]crossprod): The result of single-argument
1486 :     crossprod methods now inherits from symmetricMatrix.
1487 :    
1488 : bates 1265 2006-05-15 Douglas Bates <bates@stat.wisc.edu>
1489 :    
1490 :     * R/AllGeneric.R (lowerTriMatrix): Added (but did not export)
1491 :     generics lowerTriMatrix and upperTriMatrix along with methods for
1492 :     the Csparse virtual class. Also added a C function Csparse_band
1493 :     that implements these methods by calling cholmod_band.
1494 :    
1495 : maechler 1264 2006-05-15 Martin Maechler <maechler@stat.math.ethz.ch>
1496 :    
1497 :     * R/Tsparse.R ("["): column or row subsetting; @Dimnames[k] got
1498 :     erased when it was NULL. This led to invalid subselections!
1499 :    
1500 : bates 1259 2006-04-25 Douglas Bates <bates@stat.wisc.edu>
1501 :    
1502 :     * R/dtCMatrix.R: avoid coercion of dtCMatrix object to dgCMatrix
1503 :     in method for "t" so as not to lose the unit diagonal property.
1504 :    
1505 : bates 1257 2006-04-19 Douglas Bates <bates@stat.wisc.edu>
1506 :    
1507 :     * R/lmer.R, R/AllGeneric.R, NAMESPACE: Remove the postVar generic
1508 :     and methods. This is now an option to the ranef method for the
1509 :     mer class.
1510 :    
1511 :     * src/cs_utils.c: Ensure that the nz component is -1 for a
1512 :     compressed column-oriented matrix. Minor formatting cleanup.
1513 :    
1514 :     * man/lmer-class.Rd: Document the qqmath method for ranef.lmer
1515 :     objects.
1516 :    
1517 : maechler 1253 2006-04-19 Martin Maechler <maechler@stat.math.ethz.ch>
1518 :    
1519 :     * R/Auxiliaries.R (diagU2N): new for the solve() methods in
1520 :     * R/dtCMatrix.R: where dgC -> dgT coercion now preserves diag = "U".
1521 :    
1522 : bates 1251 2006-04-15 Douglas Bates <bates@stat.wisc.edu>
1523 :    
1524 :     * src/cs.[ch],src/cs_utils.[ch] : Added Tim Davis' CSparse library
1525 :     in cs.[ch] and utilities to interface to that code in cs_utils.[ch].
1526 :    
1527 :     * R/dtCMatrix.R, src/dtCMatrix.[ch] : CSparse-based solve methods
1528 :     for the dtCMatrix class.
1529 : maechler 1253
1530 : bates 1247 2006-04-12 Douglas Bates <bates@stat.wisc.edu>
1531 :    
1532 :     * R/pedigree.R, R/AllClass.R, NAMESPACE: added a pedigree class
1533 :     and methods for it.
1534 :    
1535 : maechler 1245 2006-04-12 Martin Maechler <maechler@stat.math.ethz.ch>
1536 :    
1537 :     * R/dgCMatrix.R: add storage.mode(.) <- "double" for "matrix"
1538 :     arguments, such that M %*% 1:6 now works
1539 :     * Tests/matprod.R: test the above
1540 :    
1541 : bates 1244 2006-04-03 Douglas Bates <bates@stat.wisc.edu>
1542 : bates 1243
1543 :     * R/lmer.R (qqmath,ranef.lmer-method): added a qqmath method for
1544 :     the ranef.lmer class.
1545 :    
1546 :     * R/AllClass.R, NAMESPACE, R/lmer.R: Added a postVar generic and
1547 :     methods to extract the posterior variances from the bVar slot.
1548 :    
1549 : maechler 1238 2006-03-30 Martin Maechler <maechler@stat.math.ethz.ch>
1550 :    
1551 :     * R/dtCMatrix.R: allow coercion from dgC* to triangular (dtC*)
1552 :     * R/dsCMatrix.R: and symmetric (dsC*) 'Csparse' matrices.
1553 :    
1554 :     * R/Tsparse.R: Tsparse* -> Csparse* coercion now works and is tested in
1555 :     * tests/simple: (extended)
1556 :    
1557 :     * R/sparseMatrix.R (isTriangular): now using much improved
1558 :     * R/Auxiliaries.R (isTriC): new triangularity check for *CMatrix
1559 :    
1560 : bates 1236 2006-03-23 Douglas Bates <bates@stat.wisc.edu>
1561 :    
1562 :     * src/dsyMatrix.c (dsyMatrix_as_dspMatrix): Propagate DimNames
1563 :     (problem report from Franklin Parlamis). This should be done
1564 : maechler 1238 generally.
1565 : bates 1236
1566 : bates 1234 2006-03-21 Douglas Bates <bates@stat.wisc.edu>
1567 :    
1568 :     * R/AllClass.R,lmer.R: Change the name of the lmer.ranef class to
1569 :     ranef.lmer (like summary.lmer). Add the coef.lmer class and
1570 :     update the plot methods.
1571 :    
1572 : bates 1232 2006-03-20 Douglas Bates <bates@stat.wisc.edu>
1573 :    
1574 :     * R/lmer.R (resid and ranef methods): Added methods for the
1575 :     "residuals" and "resid" generic but only for linear mixed model
1576 :     fits. Changed the ranef method to return a list of data frames so
1577 :     that the plot methods now work.
1578 :    
1579 : bates 1230 2006-03-16 Douglas Bates <bates@bates2>
1580 :    
1581 :     * src/dpoMatrix.c (dpoMatrix_chol): Require n > 0 in call to
1582 :     dpotrf - otherwise the BLAS on Mac OS X complains and quits.
1583 :    
1584 :     * DESCRIPTION (Date): New release
1585 :    
1586 : maechler 1228 2006-03-15 Martin Maechler <maechler@stat.math.ethz.ch>
1587 :    
1588 :     * DESCRIPTION (Version): 0.995-6 -- to be released to CRAN
1589 :    
1590 :     * data/KNex.rda: replacing 'mm' and 'y' by KNex <- list(mm=mm, y=y)
1591 :     * man/KNex.Rd: and other help files
1592 :     * tests/*.R: several ones needed adaption
1593 : bates 1352 * inst/doc/Comparisons.Rnw: ditto
1594 : maechler 1228
1595 : maechler 1226 2006-03-11 Martin Maechler <maechler@stat.math.ethz.ch>
1596 :    
1597 :     * R/dgCMatrix.R (replCmat): "[<-" methods for dgCMatrix
1598 :    
1599 :     * tests/indexing.R: tests for new [<- methods for sparse matrices.
1600 :    
1601 :     2006-03-10 Martin Maechler <maechler@stat.math.ethz.ch>
1602 :    
1603 :     * R/dgTMatrix.R (replTmat): "[<-" methods for dgTMatrix
1604 :    
1605 :     * R/Tsparse.R (.ind.prep): fix out-of-range indexing
1606 :    
1607 :     2006-03-08 Martin Maechler <maechler@stat.math.ethz.ch>
1608 :    
1609 :     * R/dMatrix.R: enable things like M [ M < 10 ]
1610 :     * R/dgeMatrix.R: implement it
1611 :    
1612 : maechler 1222 2006-03-06 Martin Maechler <maechler@stat.math.ethz.ch>
1613 :    
1614 :     * R/AllClass.R: define "summary.mer" and "*.lmer"
1615 :     * R/lmer.R (summary): summary(<mer>) computes & returns the above;
1616 :     * R/lmer.R (show): now works with summary()
1617 :    
1618 :     2006-03-04 Martin Maechler <maechler@stat.math.ethz.ch>
1619 :    
1620 :     * R/dgCMatrix.R: finally direct "Arith" dgC o dgC
1621 :     * R/Auxiliaries.R (WhichintersectInd): and other utilities to
1622 :     support the above
1623 :    
1624 : bates 1213 2006-02-07 Douglas Bates <bates@stat.wisc.edu>
1625 :    
1626 :     * R/lmer.R (lmer): fix initial values of offset and weights for glm.fit.
1627 :     Use glmFit$prior.weights for weights in a glmm.
1628 :     Allow an option usePQL = FALSE to skip the PQL steps for the
1629 :     Laplace method (and, in time, the AGQ method).
1630 :    
1631 :     * src/lmer.c (mer_factor): Move downdating and factoring of XtX
1632 :     into a separate function internal_mer_Xfactor to be able to call
1633 :     it from internal_bhat.
1634 :    
1635 : maechler 1200 2006-01-23 Martin Maechler <maechler@stat.math.ethz.ch>
1636 :    
1637 :     * tests/Class+Meth.R (tstMatrixClass): function for much better
1638 :     testing; now again of all actual classes.
1639 :    
1640 :     * src/Mutils.c (MAKE_TRIANGULAR_BODY, MAKE_SYMMETRIC_BODY):
1641 :     use macros and define make_d_matrix_* and make_i_matrix_*
1642 :     where _i_ is for the ldense routines:
1643 :    
1644 :     * src/ldense.c (ltrMatrix_as_lgeMatrix): provide functions
1645 :     * src/ldense.c (lsyMatrix_as_lgeMatrix):
1646 :    
1647 :     * R/ldenseMatrix.R: use the above in setAs(*,"lgeMatrix")
1648 :    
1649 :    
1650 : maechler 1174 2006-01-16 Martin Maechler <maechler@stat.math.ethz.ch>
1651 :    
1652 :     * R/Matrix.R (Matrix): has become much "smarter" now auto-producing
1653 :     many different kinds of matrices.
1654 :     * R/*.R: quite a few new methods were needed for R CMD check with
1655 :     new Matrix(). Very good for users playing around.
1656 :    
1657 :    
1658 : maechler 1165 2006-01-15 Martin Maechler <maechler@stat.math.ethz.ch>
1659 :    
1660 :     * src/dgeMatrix.c (dMatrix_validate): new
1661 :     * src/Mutils.c (dense_nonpacked_validate): new
1662 :    
1663 :     * src/dtrMatrix.c (dtrMatrix_validate): improved/fixed
1664 :    
1665 :    
1666 :     2006-01-14 Douglas Bates <bates@stat.wisc.edu>
1667 :    
1668 :     * R/AllClass.R (compMatrix), (generalMatrix): new virtual classes
1669 :    
1670 : bates 1123 2006-01-07 Douglas Bates <bates@stat.wisc.edu>
1671 : bates 1119
1672 : maechler 1127 * DESCRIPTION (Version): 0.99-6 released to CRAN
1673 :    
1674 : bates 1119 * src/dgBCMatrix.c (cscb_trcbsm): Fix due to Peter Dalgaard for
1675 :     segfault in cases with multiple non-nested grouping factors.
1676 :    
1677 : maechler 1109 2006-01-03 Martin Maechler <maechler@stat.math.ethz.ch>
1678 :    
1679 :     * DESCRIPTION (Version): 0.99-4 to be released to CRAN
1680 :     (Depends): also on 'utils'
1681 :    
1682 :     * R/AllClass.R (diagonalMatrix): new class with "ddi*" and "ldi*"
1683 :     * R/diagMatrix.R (Diagonal): constructor and methods for
1684 :     diagonal matrices
1685 :    
1686 :     * R/ltTMatrix.R: new "minimal methods"
1687 :    
1688 : maechler 1091 2005-12-12 Martin Maechler <maechler@stat.math.ethz.ch>
1689 :    
1690 :     * R/AllGeneric.R (tcrossprod): 2-argument version; here, and for
1691 :     all methods (and help files).
1692 :    
1693 : maechler 1084 2005-12-09 Martin Maechler <maechler@stat.math.ethz.ch>
1694 :    
1695 :     * R/Auxiliaries.R (dimNamesCheck): fixed thinko -> bug
1696 :     for case (dimn. op no_dimn.)
1697 :    
1698 :     2005-11-14 Douglas Bates <bates@stat.wisc.edu>
1699 :    
1700 : maechler 1174 * DESCRIPTION (Version): 0.99-2 released to CRAN
1701 : maechler 1084
1702 : bates 988 2005-10-21 Douglas Bates <bates@stat.wisc.edu>
1703 :    
1704 :     * R/lmer.R (simulate method): Fixed a drop=FALSE problem reported
1705 :     by Julian Faraway.
1706 :    
1707 : maechler 976 2005-10-06 Martin Maechler <maechler@stat.math.ethz.ch>
1708 :    
1709 :     * R/Auxiliaries.R (try_as): new utility
1710 :     * R/sparseMatrix.R: use try_as() in coercion to original class
1711 :    
1712 : maechler 956 2005-09-30 Martin Maechler <maechler@stat.math.ethz.ch>
1713 :    
1714 :     * src/dgCMatrix.c (double_to_csc): and dgeMatrix_to_csc()
1715 :    
1716 :     2005-09-29 Martin Maechler <maechler@stat.math.ethz.ch>
1717 :    
1718 :     * R/Auxiliaries.R (dimNamesCheck): added
1719 :    
1720 :     * R/Matrix.R (as.array), (as.vector): new
1721 :    
1722 : maechler 954 2005-09-28 Martin Maechler <maechler@stat.math.ethz.ch>
1723 :    
1724 :     * R/Matrix.R (Matrix): get logical argument 'sparse' with a smart
1725 : maechler 956 default.
1726 :     * R/AllClass.R: move 'factors' slot toplevel "Matrix";
1727 :     "pMatrix" now contains "sparseMatrix"
1728 : maechler 954
1729 : maechler 948 2005-09-26 Martin Maechler <maechler@stat.math.ethz.ch>
1730 :    
1731 :     * tests/Class+Meth.R: new tests; t(t(m)) == m
1732 :    
1733 :     * src/dtCMatrix.c (tsc_transpose): add forgotten "diag" slot
1734 :    
1735 :     * src/dsTMatrix.c (dsTMatrix_as_dsCMatrix): bad typo (segfault!)
1736 :     * src/dtTMatrix.c (dtTMatrix_as_dtCMatrix): new
1737 :    
1738 :     * R/dspMatrix.R: typo in "t" method
1739 :    
1740 : maechler 925 2005-09-18 Douglas Bates <bates@wisc.edu>
1741 :    
1742 :     * R/AllClass.R (TsparseMatrix), CsparseM* and RsparseM*
1743 :     * R/Tsparse.R: instead of R/gTMatrix.R
1744 :     * R/Csparse.R: new
1745 :     * src/Tsparse.c (Tsparse_to_Csparse): new; -> cholmod_()
1746 :     * src/Tsparse.c: new; many trivial methods calling cholmod_()
1747 :     * src/Csparse.c (Csparse_to_Tsparse), transpose, (mat|cross)prod:
1748 :     via cholmod
1749 :    
1750 :     2005-09-16 Martin Maechler <maechler@stat.math.ethz.ch>
1751 :    
1752 :     * R/Auxiliaries.R (non0ind): new function using new C code
1753 :     * src/dgCMatrix.c (compressed_non_0_ij): new utility
1754 :    
1755 : bates 917 2005-09-15 Douglas Bates <bates@localhost.localdomain>
1756 :    
1757 :     * src/chm_common.h: header file required by all C sources that
1758 : maechler 1174 call CHOLMOD functions. It defines a cholmod_common structure
1759 : bates 917 called 'c' whose address is passed as the last argument to
1760 :     (virtually) every CHOLMOD function.
1761 :    
1762 :     * src/Pattern.c: Simple example of the use of CHOLMOD.
1763 :    
1764 :     * src/init.c: initialize and finalize the cholmod_common structure.
1765 :    
1766 :     * src/Makefile: Added source packages CHOLMOD UMFPACK AMD COLAMD
1767 :     LDL and CCOLAMD from the U. of Florida sparse matrix library.
1768 :    
1769 : maechler 908 2005-09-08 Martin Maechler <maechler@stat.math.ethz.ch>
1770 :    
1771 :     * inst/test-tools.R: new file collecting the utility functions used
1772 :     in ./tests/*.R
1773 :    
1774 :     * R/ddenseMatrix.R (cbind2): new methods for "numeric" and "matrix"
1775 :     * R/Matrix.R (cbind2): methods for NULL and missing
1776 :    
1777 : maechler 886 2005-08-31 Martin Maechler <maechler@stat.math.ethz.ch>
1778 :    
1779 :     * R/AllClass.R: new "index" class for "[" and "[<-":
1780 :     First cut at "symmetricMatrix" and "triangularMatrix"
1781 :     * R/gTMatrix.R (.ind.prep): new function;
1782 : maechler 1174 Logical and character indexing now work too.
1783 : maechler 886 * R/Matrix.R: cheap "[<-" methods for denseMatrix now work
1784 :     * tests/indexing.R: new, including *.Rout.save
1785 :     * tests/dgTMatrix.R: new
1786 :    
1787 : bates 876 2005-08-29 Douglas Bates <bates@wisc.edu>
1788 :    
1789 :     * src/dgTMatrix.c (graphNEL_as_dgTMatrix): Corrected the position
1790 :     indicator pos not being updated. Also enforced upper triangular
1791 :     for symmetric case. Need to coerce edges component of elements of
1792 :     edge list - grr! (Why don't they define their classes cleanly?)
1793 :    
1794 : maechler 871 2005-08-26 Martin Maechler <maechler@stat.math.ethz.ch>
1795 :    
1796 :     * R/Matrix.R: added first "[<-" methods; not yet functional
1797 : bates 1352 * R/denseMatrix.R: ditto
1798 : maechler 871 * man/Subassign-methods.Rd: new help file for these
1799 :    
1800 :     2005-08-25 Martin Maechler <maechler@stat.math.ethz.ch>
1801 :    
1802 :     * DESCRIPTION (Version): 0.98-6
1803 :    
1804 :     * R/denseMatrix.R: new file for "[" fallback methods for all dense
1805 :     matrices.
1806 :    
1807 : maechler 868 2005-08-19 Martin Maechler <maechler@stat.math.ethz.ch>
1808 :    
1809 :     * src/lgCMatrix.c (lcsc_to_matrix): new; need for
1810 :     as( <logical>, "matrix")
1811 :    
1812 :     * R/pMatrix.R: coercion to "lgTMatrix"
1813 :    
1814 :     * R/gTMatrix.R: new virtual class to define "[" methods for.
1815 :     * man/gTMatrix-class.Rd:
1816 :     * General slight re-organization of where "[" methods are defined.
1817 :     more to come.
1818 :    
1819 : maechler 871 2005-08-18 Douglas Bates <bates@wisc.edu>
1820 : maechler 868
1821 : maechler 1174 * DESCRIPTION (Version): 0.98-5 released to CRAN
1822 : maechler 871
1823 :     * src/dgTMatrix.c (graphNEL_as_dgTMatrix): add first graphNEL methods
1824 :     * .....
1825 :    
1826 : bates 863 2005-08-18 Douglas Bates <bates@localhost.localdomain>
1827 :    
1828 :     * R/lmer.R: Corrected naming scheme in mcmcsamp to work with lmer
1829 :     or glmer objects.
1830 :    
1831 : maechler 860 2005-08-17 Martin Maechler <maechler@stat.math.ethz.ch>
1832 :    
1833 :     * DESCRIPTION (Version): 0.98-4 : upload to CRAN
1834 :    
1835 :     2005-08-16 Douglas Bates <bates@localhost.localdomain>
1836 :    
1837 :     * R/HBMM.R: finish re-writing R-only code.
1838 :    
1839 : bates 854 2005-08-15 Douglas Bates <bates@localhost.localdomain>
1840 :    
1841 :     * man/externalFormats.Rd: move documentation for writeHB and
1842 :     writeMM here.
1843 :    
1844 :     * src/mmio.c: replace inclusion of <malloc.h> by <stdlib.h>
1845 :     (suggested by Paul Roecker).
1846 :    
1847 :     * tests/validObj.R (assertError): Comment out test that is failing
1848 :     after recent changes in r-devel.
1849 :    
1850 : maechler 860
1851 : maechler 848 2005-08-11 Martin Maechler <maechler@stat.math.ethz.ch>
1852 :    
1853 :     * R/AllClass.R: intermediate virtual class "denseMatrix"
1854 :     * man/denseMatrix-class.Rd
1855 :     * NAMESPACE: export it, and also export
1856 :     * man/unused-classes.Rd: "iMatrix", "zMatrix" and "ldenseMatrix"
1857 :    
1858 : bates 846 2005-08-10 Douglas Bates <bates@wisc.edu>
1859 :    
1860 : maechler 848 * DESCRIPTION (Version): 0.98-3 to CRAN
1861 :    
1862 : bates 846 * src/dtrMatrix.c (dtrMatrix_validate): fixed up validation and
1863 :     matrix_solve code (which was really, really wrong).
1864 :    
1865 : bates 835 2005-08-07 Douglas Bates <bates@wisc.edu>
1866 : maechler 834
1867 :     * DESCRIPTION (Version): 0.98-2
1868 :    
1869 :     * R/HBMM.R (readHB), (readMM): read Matrix Market formats
1870 :    
1871 :     * R/lmer.R (abbrvNms): new
1872 :     * R/lmer.R (mcmcsamp): allow transformed parameters
1873 : bates 835 * src/HBMM.c (Matrix_writeMatrixMarket): Added read/write routines
1874 :     for the Harwell-Boeing and the MatrixMarket formats.
1875 : maechler 834
1876 :     2005-08-04 Martin Maechler <maechler@stat.math.ethz.ch>
1877 :    
1878 :     * man/dtrMatrix-class.Rd: add examples
1879 : bates 835 * man/dtpMatrix-class.Rd: ditto; plus note about PROBLEM
1880 : maechler 834
1881 :     * TODO: note the dtpMatrix (docu) bug
1882 :    
1883 :     * R/zzz.R (.onLoad): assignInNamespace("as.matrix", *, "base")
1884 :     in order to ensure that new as.matrix() is used by old functions,
1885 :     e.g., svd(), qr(), eigen(), dist(),..;
1886 :     apply(), also matplot() or pairs().
1887 :    
1888 :    
1889 :     2005-08-03 Martin Maechler <maechler@stat.math.ethz.ch>
1890 :    
1891 :     * R/lmer.R: add 'fixme' comments and move the linear vs glm check;
1892 :     add comments about 'control' / lmerControl() arguments
1893 :    
1894 : bates 835 2005-07-27 Douglas Bates <bates@wisc.edu>
1895 : bates 820
1896 : bates 835 * man/sleepstudy.Rd: Added the sleep data set.
1897 : maechler 1174 * DESCRIPTION (Version): 0.98-1 released to CRAN
1898 : bates 820
1899 : bates 835 2005-07-12 Douglas Bates <bates@wisc.edu>
1900 : maechler 834 * man/sleepstudy.Rd: Added the sleep data set.
1901 :    
1902 : bates 809 * R/lmer.R (glmmMCMC): Added PACKAGE = "Matrix" in a couple of
1903 :     .Call calls that were producing spurious output.
1904 :    
1905 : bates 835 2005-07-05 Douglas Bates <bates@wisc.edu>
1906 : bates 801
1907 :     * R/lmer.R (lmer): stored updated variance component estimates in
1908 :     mer object for the generalized model. (Bug reported by Renaud
1909 :     Lancelot).
1910 :    
1911 : bates 835 2005-07-03 Douglas Bates <bates@wisc.edu>
1912 : bates 794
1913 :     * src/lmer.c (glmer_devAGQ): Added AGQ for single grouping factor,
1914 :     unidimensional case.
1915 :    
1916 : bates 835 2005-06-08 Douglas Bates <bates@wisc.edu>
1917 : maechler 791
1918 :     * DESCRIPTION (Version): 0.96-1
1919 :    
1920 : maechler 1174 * moved lmer-class' R and C code moved from lme4 to here
1921 : maechler 791
1922 : bates 835 2005-06-04 Douglas Bates <bates@wisc.edu>
1923 : bates 763
1924 :     * R/dgCMatrix.R: Call to csc_matrix_mm used undefined arguments
1925 :     (reported by Guissepe Ragusa <gragusa@ucsd.edu>)
1926 :    
1927 : bates 835 2005-06-02 Douglas Bates <bates@wisc.edu>
1928 : bates 763
1929 :     * src/Makefile.win: Forgot to update this when Makefile changed.
1930 :    
1931 : bates 835 2005-05-11 Douglas Bates <bates@wisc.edu>
1932 : bates 726
1933 :     * src/dgCMatrix.c (csc_transpose): Simplified function fixing a
1934 :     bug reported by Kurt Hornik and Michael Hahsler.
1935 :    
1936 : bates 835 2005-05-10 Douglas Bates <bates@wisc.edu>
1937 : bates 725
1938 :     * src/lgCMatrix.c (Matrix_lgClgCmm): Implementation of methods for
1939 :     logical sparse matrices. These will also be used in the symbolic
1940 :     analysis for lmer objects.
1941 :    
1942 :     * src/dsCMatrix.c (dsCMatrix_matrix_solve): Copied the dimensions
1943 :     of b to the result. Fixes bug reported by Jean.Coursol@math.u-psud.fr
1944 : maechler 791
1945 : bates 835 2005-05-06 Douglas Bates <bates@wisc.edu>
1946 : bates 714
1947 :     * src/dgeMatrix.c (dgeMatrix_colsums): Added an implementation of
1948 :     colMeans, colSums, rowMeans and rowSums.
1949 :    
1950 : bates 835 2005-04-18 Douglas Bates <bates@wisc.edu>
1951 : bates 692
1952 :     * src/lgCMatrix.[ch]: code for _validate method and stub for
1953 :     multiplication operation.
1954 :    
1955 :     * src/dgeMatrix.c (dgeMatrix_matrix_solve): Passing wrong argument
1956 :     to dgetrs.
1957 :    
1958 :     * src/init.c: Fix cut-and-paste error in definition of
1959 :     dgeMatrix_matrix_solve
1960 :    
1961 :     * src/{many files}: Tighten code by using ALLOC_SLOT.
1962 :    
1963 : bates 835 2005-04-15 Douglas Bates <bates@wisc.edu>
1964 : bates 692
1965 :     * R/AllClass.R: Add lgTMatrix and lgCMatrix classes
1966 :    
1967 :     * DESCRIPTION: Eliminate import of stats.
1968 :    
1969 : maechler 791
1970 : bates 835 2005-04-06 Douglas Bates <bates@wisc.edu>
1971 : bates 692
1972 :     * R/AllClass.R : add logical sparse matrix classes
1973 :    
1974 : maechler 687 2005-04-01 Martin Maechler <maechler@stat.math.ethz.ch>
1975 :    
1976 :     * R/dgTMatrix.R: add "[" method for triplet matrices
1977 :     * R/sparseMatrix.R: and other sparse ones; --> add show() for sparse
1978 :    
1979 : bates 835 2005-03-31 Douglas Bates <bates@wisc.edu>
1980 : maechler 687
1981 :     * DESCRIPTION (Version): release 0.95-5 to CRAN
1982 :    
1983 :     * R/dMatrix.R: add %*%, crossprod and solve "fallback" methods
1984 :     * R/sparseMatrix.R: %*%, crossprod()
1985 :     * R/dgeMatrix.R: more "fallback" methods for numeric/dense matrices
1986 :     * man/*.Rd: move method definitions to 'Matrix' and 'dMatrix'
1987 :     * src/lmer.c (lmer_fitted): fix thinko
1988 :    
1989 : maechler 676 2005-03-26 Martin Maechler <maechler@stat.math.ethz.ch>
1990 :    
1991 :     * R/AllClass.R: add two virtual sparse classes ``on top''
1992 :    
1993 :     2005-03-24 Martin Maechler <maechler@stat.math.ethz.ch>
1994 :    
1995 :     * R/AllClass.R (setClass): use "VIRTUAL" for the virtual classes;
1996 :     correspondingly fix examples and tests/ since new()
1997 :     doesn't work for virtual classes.
1998 :    
1999 : maechler 658 2005-03-17 Martin Maechler <maechler@stat.math.ethz.ch>
2000 :    
2001 :     * R/Matrix.R (as.matrix): method and one for unname()
2002 :     * tests/dpoMatrix.R: tests should now be less platform dependent;
2003 :     also run for R 2.1.0; using as.matrix()
2004 :    
2005 : bates 835 2005-03-15 Douglas Bates <bates@wisc.edu>
2006 : maechler 658
2007 :     * R/pMatrix.R: "pMatrix" class added
2008 :     * ....
2009 :    
2010 : bates 835 2005-03-14 Douglas Bates <bates@wisc.edu>
2011 : bates 645
2012 :     * R/dtpMatrix.R: Add unpack method and an example.
2013 :    
2014 :     * src/dsyMatrix.c (dsyMatrix_trf): Add BunchKaufman factorization
2015 :     of general symmetric matrices and associated S4 methods.
2016 :    
2017 : maechler 658 2005-03-10 Martin Maechler <maechler@stat.math.ethz.ch>
2018 :     +
2019 :     2005-03-05 Martin Maechler <maechler@stat.math.ethz.ch>
2020 :    
2021 :     * R/dgeMatrix.R (setAs): and many other files: more coercion,
2022 :     crossprod() and "%*%" methods added; tests, too.
2023 :     * tests/matprod.R: new, for testing these
2024 :    
2025 : bates 835 2005-03-03 Douglas Bates <bates@wisc.edu>
2026 : bates 599
2027 :     * src/lmer.c (lmer_fitted): Added.
2028 :    
2029 : bates 835 2005-03-02 Douglas Bates <bates@wisc.edu>
2030 : bates 596
2031 :     * R/dsTMatrix.R: Conversion from dsTMatrix to dsCMatrix
2032 :    
2033 : bates 835 2005-02-28 Douglas Bates <bates@wisc.edu>
2034 : bates 582
2035 :     * src/*.c,po/,inst/po: Internationalization and localization of
2036 :     the package.
2037 :    
2038 :     * src/ldl.[ch]: Removed these as their contents are referenced in the
2039 :     R_ldl.c file.
2040 :    
2041 :     * src/flame.[ch]: Removed these source files.
2042 : maechler 658
2043 : bates 582 * src/dtrMatrix.c (make_array_triangular): Move to Mutils
2044 :    
2045 :     * src/LU.[ch],src/init.c: absorb in factorizations
2046 :    
2047 :     * src/Mutils.h: prepare for internationalization
2048 :    
2049 :     * src/cblas.h: move the enum definitions to Mutils.h and remove
2050 :     this file
2051 :    
2052 : maechler 578 2005-02-26 Martin Maechler <maechler@stat.math.ethz.ch>
2053 :    
2054 : maechler 579 * R/dgeMatrix.R: provide "dimnames" and "dimnames<-" methods
2055 :    
2056 :     * R/dtrMatrix.R: fix t() method
2057 :    
2058 : maechler 578 * R/dgeMatrix.R: define group methods "Arith", "Math", "Math2"
2059 : maechler 658 * NAMESPACE: export them (and import generics from "methods")
2060 : maechler 578 * tests/group-methods.R : and test them.
2061 :    
2062 :     * src/dtrMatrix.c (dtrMatrix_as_dgeMatrix): prevent seg.fault in
2063 :     border case
2064 :    
2065 :     2005-02-24 Douglas Bates <bates@stat.wisc.edu>
2066 :    
2067 : maechler 658 * DESCRIPTION (Version): 0.95-2 released to CRAN
2068 : maechler 578
2069 :     * src/dgBCMatrix.c:
2070 :     * src/lmer.c: many changes
2071 :     * ...
2072 :    
2073 : maechler 512 2005-02-04 Martin Maechler <maechler@stat.math.ethz.ch>
2074 :    
2075 :     * R/Matrix.R: add more sophisticated show() method.
2076 :    
2077 : maechler 578 2005-02-02 Douglas Bates <bates@stat.wisc.edu>
2078 :    
2079 :     * */* : almost complete reorganization of classes.
2080 :    
2081 : bates 835 2005-01-26 Douglas Bates <bates@wisc.edu>
2082 : bates 460
2083 :     * R/AllGeneric.R: Added matrix exponential generic expm and a method
2084 :     for the geMatrix class.
2085 :    
2086 : bates 835 2005-01-24 Douglas Bates <bates@wisc.edu>
2087 : bates 460
2088 :     * src/Makefile (clean): Remove *.a and *.so
2089 :    
2090 :     * man/cscBlocked-class.Rd: Remove reference to the lmer-class.
2091 :    
2092 : bates 835 2005-01-23 Douglas Bates <bates@wisc.edu>
2093 : bates 460
2094 : maechler 658 * src/lmer.c (Lind): Definition of Lind was backwards. This only
2095 : bates 460 had an effect in cases with more than 2 grouping factors.
2096 :    
2097 : bates 835 2005-01-03 Douglas Bates <bates@wisc.edu>
2098 : bates 415
2099 :     * src/lmeRep.c (lmer_variances): change from lmeRep to lmer
2100 :    
2101 : bates 835 2004-12-23 Douglas Bates <bates@wisc.edu>
2102 : bates 410
2103 :     * src/init.c (R_init_Matrix): Reorder calls to R_registerRoutines
2104 :     and R_useDynamicSymbols (suggested by B.D.Ripley).
2105 :    
2106 : bates 835 2004-12-14 Douglas Bates <bates@wisc.edu>
2107 : bates 392
2108 :     * R/sscMatrix.R: Add determinant methods
2109 :    
2110 :     * src/triplet.[ch],src/init.c (triplet_to_matrix): Add a coercion
2111 :     for tripletMatrix to matrix.
2112 :    
2113 : bates 835 2004-12-13 Douglas Bates <bates@wisc.edu>
2114 : bates 388
2115 : bates 392 * R/AllClass.R (.onLoad): Eliminate the bbCrosstab class, which is
2116 :     no longer used.
2117 :    
2118 : bates 388 * src/R_ldl.c: Created an R-specific version of the ldl.[ch] files
2119 :     with dynamic allocation of scratch arrays.
2120 :    
2121 :     * src/ssclme.c (ssclme_copy_ctab): Fixed bug in creation of ZtZ
2122 :     for multivariate random effects with multiple grouping factors.
2123 :     Fixes part but not all of #15.
2124 :    
2125 : bates 835 2004-12-03 Douglas Bates <bates@wisc.edu>
2126 : bates 375
2127 :     * src/lmeRep.c (lmeRep_factor): order of operations for multiple
2128 :     scalar grouping factors corrected.
2129 :    
2130 : bates 835 2004-11-29 Douglas Bates <bates@wisc.edu>
2131 : bates 375
2132 :     * src/bCrosstab.c: remove diag_update which is no longer used
2133 :    
2134 : bates 835 2004-11-16 Douglas Bates <bates@wisc.edu>
2135 : bates 350
2136 :     * src/Metis_utils.c: Move metis.h include to C sources so that the
2137 :     .h file can be included.
2138 :    
2139 : bates 835 2004-11-12 Douglas Bates <bates@wisc.edu>
2140 : bates 342
2141 : bates 350 * src/LU.c,geMatrix.c,trMatrix.c, etc.:
2142 : bates 342 Complete allocation of slots in NEW_OBJECT.
2143 :    
2144 :     * src/Mutils.h: Moved list of symbols to an include file
2145 :    
2146 : bates 835 2004-11-11 Douglas Bates <bates@wisc.edu>
2147 : bates 342
2148 :     * src/geMutils.c (Matrix_init): remove unused function
2149 :    
2150 : bates 835 2004-11-10 Douglas Bates <bates@wisc.edu>
2151 : bates 342
2152 :     * src/cscMatrix.c (csc_to_imagemat): removed unused function
2153 :    
2154 : bates 835 2004-11-05 Douglas Bates <bates@wisc.edu>
2155 : bates 327
2156 :     * src/Makefile.win (SOURCES_C): Keep consistent with Makefile
2157 :    
2158 : bates 835 2004-10-27 Douglas Bates <bates@wisc.edu>
2159 : bates 303
2160 :     * R/pdmatrix.R: remove PACKAGE="Matrix" in .Call calls
2161 :    
2162 : bates 835 2004-10-04 Douglas Bates <bates@wisc.edu>
2163 : bates 296
2164 :     * src/init.c: Created R_init_Matrix and added registration of C
2165 :     routines.
2166 :    
2167 : bates 835 2004-10-02 Douglas Bates <bates@wisc.edu>
2168 : bates 283
2169 :     * R/tripletMatrix.R: Force a require(lattice) for the image methods.
2170 :    
2171 : bates 835 2004-06-15 Douglas Bates <bates@wisc.edu>
2172 : bates 229
2173 :     * man/trMatrix-class.Rd: Escape the % chars in .Rd files.
2174 :    
2175 : bates 111 2004-04-20 Douglas Bates <bates@stat.wisc.edu>
2176 :    
2177 :     * src/Makefile.win ($(SHLIB)): Modifications per Uwe Ligges.
2178 :    
2179 : bates 109 2004-04-19 Douglas Bates <bates@stat.wisc.edu>
2180 :    
2181 :     * src/ssclme.c (ssclme_update_mm): fix logic error in
2182 :     ssclme_update_mm
2183 :    
2184 : bates 105 2004-04-18 Douglas Bates <bates@stat.wisc.edu>
2185 :    
2186 :     * src/ssclme.c (ssclme_coef, ssclme_coefGets): Create consistency
2187 :     in the order of unconstrained and constrained parameters.
2188 :     (ssclme_gradient): Added the gradients (not yet correct for
2189 :     multidimensional, unconstrained case).
2190 :    
2191 : bates 78 2004-04-14 Douglas Bates <bates@stat.wisc.edu>
2192 :    
2193 :     * src/ssclme.c (ssclme_EMsteps): Fix logic in REML update
2194 :    
2195 :     * src/Makefile.win: Remove unneeded ranlib call
2196 :    
2197 : bates 71 2004-04-12 Douglas Bates <bates@stat.wisc.edu>
2198 :    
2199 :     * DESCRIPTION (Version): New release
2200 :    
2201 :     * src/Makefile.win: Update Makefile.win to umfpack removal.
2202 :    
2203 : bates 49 2004-04-05 Douglas Bates <bates@bates2_home>
2204 :    
2205 :     * src/triplet_to_col.c: Create triplet_to_col as a native
2206 : maechler 658 function, not the version from umfpack. There were problems with
2207 : bates 49 the configuration of UMFPACK for 64-bit processors and there was
2208 :     only one umfpack routine being used so I moved it here.
2209 :    
2210 : bates 45 2004-04-04 Douglas Bates <bates@bates2_home>
2211 :    
2212 :     * src/ssclme.c (ssclme_variances): New function.
2213 :    
2214 : bates 28 2004-03-28 Douglas Bates <bates@bates2_home>
2215 :    
2216 :     * src/ssclme.c (ssclme_fitted): Added function.
2217 :    
2218 : bates 22 2004-03-27 Douglas Bates <bates@bates2_home>
2219 :    
2220 :     * src/ssclme.c (ssclme_transfer_dimnames): Add new function to
2221 :     store the dimnames in the XtX and bVar slots
2222 :     (ssclme_update_mm): Change the dimensions of the bVar slot
2223 :     components and the returned value from ssclme_ranef.
2224 :    
2225 : bates 10 2004-03-18 Douglas Bates <bates@stat.wisc.edu>
2226 :    
2227 :     * R/{pdMat.R,pdIdent.R,pdLogChol.R,pdMatrixLog.R,pdNatural.R},
2228 :     src/{pdMat.c,pdIdent.c,pdLogChol.c,pdNatural.c},
2229 :     tests/{pdCompSymm.R,pdDiag.R,pdIdent.R,pdLogChol.R,pdNatural.R},
2230 :     man/{pdMat-class.Rd,pdmatrix-class.Rd,corrmatrix-class.Rd,
2231 :     pdDiag-class.Rd,pdIdent-class.Rd,pdNatural-class.Rd,
2232 :     pdLogChol-class.Rd,coefGets.Rd,pdCompSymm-class.Rd,
2233 :     pdfactor-class.Rd,pdFactor.Rd,pdMatrix.Rd,
2234 :     pdBlocked-class.Rd},AllClass.R,AllGeneric.R:
2235 :     Moved the pdMat classes from the lme4 package.
2236 :    
2237 :     2004-03-02 Douglas Bates <bates@stat.wisc.edu>
2238 :    
2239 :     * man/ssclme-class.Rd: Update definition and documentation of the
2240 :     ssclme class to include the DIsqrt slot.
2241 :    
2242 :     * src/ssclme.c (ssclme_deviance): Modify order of computation
2243 :     (much faster using dsyrk, a level 3 BLAS routine).
2244 :    
2245 :     * src/Makefile (SUBLIBS): Change definition (K. Hornik)
2246 :    
2247 :     2004-02-28 Douglas Bates <bates@stat.wisc.edu>
2248 :    
2249 :     * tests/ssclme.R: Modify the test to account for the permutation
2250 :     of the levels of the grouping factors.
2251 :    
2252 :     2004-02-23 Douglas Bates <bates@stat.wisc.edu>
2253 :    
2254 :     * R/ssclme.R,src/ssclme.c (ssclme): Move slots of sscCrosstab slot
2255 :     directly into the ssclme class definition.
2256 :    
2257 :     2004-02-22 Douglas Bates <bates@stat.wisc.edu>
2258 :    
2259 :     * DESCRIPTION (Date): New release
2260 :    
2261 :     * man/ssclme-class.Rd: new file.
2262 :    
2263 :     * src/ssclme.c (ssclme_loglik): major revisions in design. It
2264 :     works and it's fast!
2265 :    
2266 :     2004-02-17 Douglas Bates <bates@stat.wisc.edu>
2267 :    
2268 :     * src/taucs/Makefile.win (lib): Change "ar" to "$(AR)" (B.Ripley)
2269 :    
2270 :     2004-02-16 Douglas Bates <bates@stat.wisc.edu>
2271 :    
2272 :     * DESCRIPTION (Date): New release
2273 :    
2274 :     * NAMESPACE: Don't export ssclme.
2275 :    
2276 :     * data/ScotsSec.rda, man/ScotsSec.Rd: Add Scottish secondary
2277 :     school data.
2278 :    
2279 :     2004-02-11 Douglas Bates <bates@stat.wisc.edu>
2280 :    
2281 :     * src/sscCrosstab.c (sscCrosstab): Added a row to the incidence to
2282 :     keep track of the fixed-effects and the response. Counts also
2283 :     gets an extra element, which is always one.
2284 :    
2285 :     * src/ldl.c: Include these routines from Tim Davis' LDL package.
2286 :    
2287 :     2004-02-10 Douglas Bates <bates@stat.wisc.edu>
2288 :    
2289 :     * src/cscMatrix.c (csc_transpose): new function
2290 :    
2291 :     * src/Mutils.c (csc_sort_columns): perm/iperm confusion corrected
2292 :     (csc_components_transpose): new function
2293 :    
2294 :     2004-02-06 Douglas Bates <bates@stat.wisc.edu>
2295 :    
2296 :     * src/triplet.c (triplet_validate): Fix Dim slot on generated
2297 :     triplets
2298 :    
2299 :     2004-01-30 Douglas Bates <bates@stat.wisc.edu>
2300 :    
2301 :     * R/sscCrosstab.R (sscCrosstab): Added sscCrosstab generator function.
2302 :    
2303 :     * src/LU.h (MATRIX_LU_H): Add #ifndef #define ... #endif to this
2304 :     and all other .h files in src.
2305 :    
2306 :     * src/Makefile.win: This and other Makefile.win files contributed
2307 :     by Brian Ripley.
2308 :    
2309 :     2004-01-27 Douglas Bates <bates@stat.wisc.edu>
2310 :    
2311 :     * R/syMatrix.R: Added methods for "%*%".
2312 :    
2313 :     * R/Hilbert.R (Hilbert): Changed Hilbert function to return a
2314 :     poMatrix object.
2315 :    
2316 :     2004-01-26 Douglas Bates <bates@stat.wisc.edu>
2317 :    
2318 :     * man/sscChol-class.Rd,man/mm.Rd,man/y.Rd: Added man pages.
2319 :    
2320 :     2004-01-25 Douglas Bates <bates@bates2_home>
2321 :    
2322 :     * inst/doc/Introduction.Rnw,Comparisons.Rnw: Added vignettes.
2323 :    
2324 :     * R/csc.R: Convert all cscMatrix classes to use Dim slot instead
2325 :     of nrow.
2326 :    
2327 :     2003-12-31 Douglas Bates <bates@stat.wisc.edu>
2328 :    
2329 :     * src/taucs/taucs.h: Moved taucs.h, amd.h, and umfpack.h into
2330 :     subdirectories.
2331 :    
2332 :     2003-12-08 Douglas Bates <bates@stat.wisc.edu>
2333 :    
2334 :     * src/taucs.h: Accidently referred to global header files
2335 :     instead of local files.
2336 :    
2337 :     2003-12-04 Douglas Bates <bates@stat.wisc.edu>
2338 :    
2339 :     * R/AllClass.R: Lots of changes. Removed all the lapack++ code
2340 :     and methods and replaced all classes with S4 classes.
2341 :    
2342 :     2003-04-19 Douglas Bates <bates@stat.wisc.edu>
2343 :    
2344 :     * R/det.R,man/det.Rd: Change name of det generic to determinant
2345 :    
2346 :     * src/R_LapackPP.cc: Change method of calculating determinants
2347 :    
2348 :     2003-02-03 Douglas Bates <bates@stat.wisc.edu>
2349 :    
2350 :     * DESCRIPTION (Version): removed empty data directory as requested
2351 :     by CRAN maintainers. Changed version number and date.
2352 :    
2353 :     2002-10-23 Douglas Bates <bates@stat.wisc.edu>
2354 :    
2355 :     * src/laindex.h: Applied patches from Brian Ripley for compilation
2356 :     under Windows.
2357 :    
2358 :     * Added configure.win and src/Makevars.win as requested by Brian
2359 :     Ripley.
2360 :    
2361 :     2002-05-03 Douglas Bates <bates@stat.wisc.edu>
2362 :    
2363 :     * src/lamatrix.h: Removing pre-1.2.0 compatibility code per Kurt
2364 :     Hornik.
2365 :    
2366 :     2002-04-24 Douglas Bates <bates@stat.wisc.edu>
2367 :    
2368 :     * configure.ac: Replaced configure.in with configure.ac
2369 :     contributed by Kurt Hornik.
2370 :    
2371 :     * aclocal.m4 (ac_clean_files): Replaced this with Kurt Hornik's
2372 :     version for R-1.5.0
2373 :    
2374 : maechler 512
2375 : bates 10 2001-12-10 Douglas Bates <bates@stat.wisc.edu>
2376 :    
2377 :     * man/eigen.Rd: Removed the .Alias in the example

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