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Annotation of /pkg/ChangeLog

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1 : maechler 2018 2007-08-01 Martin Maechler <maechler@stat.math.ethz.ch>
2 :    
3 :     * src/dtrMatrix.c (dtrMatrix_matrix_mm): fix dimensionality check (!)
4 :     * tests/matprod.R: regr.test for it
5 :    
6 : maechler 2011 2007-07-20 Martin Maechler <maechler@stat.math.ethz.ch>
7 :    
8 :     * R/dMatrix.R: fix from Brian for Math2(., digits = "missing")
9 :     * tests/group-methods.R: and regression-test it
10 :    
11 : bates 2008 2007-07-19 19:45 Douglas Bates <bates@stat.wisc.edu>
12 :    
13 :     * [r4642] inst/include/Matrix.h, inst/include/Matrix_stubs.c,
14 :     inst/include/cholmod.h, src/chm_common.c, src/init.c: Export
15 :     triplet_to_sparse, documentation, use typedefs
16 : maechler 2011
17 : maechler 2005 2007-07-18 Martin Maechler <maechler@stat.math.ethz.ch>
18 :    
19 :     * man/dpoMatrix-class.Rd: added 'corMatrix' example
20 :    
21 :     * src/dsyMatrix.[ch] (dsyMatrix_as_matrix): new 'keep_dimnames' arg
22 :     * src/dtrMatrix.[ch] (dtrMatrix_as_matrix): ditto
23 :     * src/init.c, R/dsyMatrix.R, R/dtrMatrix.R, R/lgTMatrix.R: ditto
24 :    
25 :     * R/lsparseMatrix.R: bug fix in "all" method
26 :     * R/Ops.R (.do.Logic.lsparse): "|" bug in borderline case
27 :    
28 :     * R/dsyMatrix.R (coerce->dsTMatrix): (i,j) slots should *not* have names
29 :     * R/ngTMatrix.R (coerce->ngTMatrix): ditto;
30 :     + matrix |-> nMatrix coercion
31 :     * R/pMatrix.R: + setAs() to dMatrix and from nMatrix
32 :     * man/pMatrix-class.Rd: ditto
33 :    
34 :     * R/Matrix.R (Summary): method for non-dMatrix
35 :    
36 :     * tests/Class+Meth.R (extraValid): new check about "dirty" slots
37 :     * tests/Class+Meth.R (tstMatrixClass): test norm(.);
38 :     test all Summary methods.
39 :    
40 :     2007-07-16 Martin Maechler <maechler@stat.math.ethz.ch>
41 :    
42 :     * R/dgeMatrix.R (norm, rcond): methods for 'matrix'
43 :    
44 :     2007-07-14 Martin Maechler <maechler@stat.math.ethz.ch>
45 :    
46 :     * R/sparseMatrix.R (norm): simple methods for sparseMatrix
47 :    
48 :     * R/pMatrix.R (t?crossprod): methods for pMatrix
49 :    
50 : bates 1987 2007-07-10 Douglas Bates <bates@stat.wisc.edu>
51 :    
52 :     * src/dgeMatrix.c (dgeMatrix_colsums): Get the logic straight.
53 :    
54 : bates 1975 2007-07-09 20:45 Douglas Bates <bates@stat.wisc.edu>
55 :    
56 :     * [r4579] src/dgeMatrix.c: Untangle horrible code in dgeMatrix_colsums
57 : maechler 2005 trying to fix a subtle bug - which has been somewhere else.
58 : bates 1975
59 :     2007-07-09 19:43 Martin Maechler <maechler@stat.math.ethz.ch>
60 :    
61 :     * [r4578] src/dgeMatrix.c: "cleaned" dgeMatrix_colsums() - but did not
62 :     solve the bug
63 :    
64 : maechler 1968 2007-07-08 Martin Maechler <maechler@stat.math.ethz.ch>
65 : bates 1964
66 : maechler 1968 * src/dgCMatrix.c (compressed_to_TMatrix):
67 :    
68 :     2007-07-07 Martin Maechler <maechler@stat.math.ethz.ch>
69 :    
70 :     * src/Csparse.c (Rsparse_validate): new, to have some validity
71 :     checking for RsparseMatrix
72 :     * src/dgCMatrix.c (xRMatrix_validate): ditto
73 :     * src/dtCMatrix.c (tRMatrix_validate): ditto
74 :    
75 :     2007-07-07 Douglas Bates <bates@stat.wisc.edu>
76 :    
77 : bates 1964 * [r4567] R/AllClass.R: Slots already in RsparseMatrix were redefined in
78 :     lgRMatrix
79 :     * [r4568] DESCRIPTION: Prepare for bug-fix release
80 : bates 1966 * [r4570] src/CHOLMOD/Check/cholmod_write.c: Include cholmod_matrixops.h
81 :     for declaration of cholmod_symmetry
82 : maechler 1968
83 : maechler 1961 2007-07-06 Martin Maechler <maechler@stat.math.ethz.ch>
84 :    
85 :     * DESCRIPTION (Version): 0.999375 merged into the trunk; ready for
86 :     release.
87 :    
88 : maechler 1960 2007-07-06 14:11 Douglas Bates <bates@stat.wisc.edu>
89 :    
90 :     * [r4559] src/iohb.c, src/iohb.h: Remove Harwell-Boeing input/output
91 :     functions - no longer used
92 :     * [r4560] src/HBMM.c, src/Mutils.c, src/dgTMatrix.c, src/dgeMatrix.c,
93 :     src/dspMatrix.c, src/dsyMatrix.c, src/dtCMatrix.c,
94 :     src/factorizations.c, src/sparseQR.c: Replace most calls to Calloc by
95 :     Alloca
96 :    
97 :     2007-07-06 13:14 Martin Maechler <maechler@stat.math.ethz.ch>
98 :    
99 :     * [r4558] inst/doc/Comparisons.Rnw, src/CHMfactor.c, src/Csparse.c,
100 :     src/Tsparse.c, src/chm_common.c, src/chm_common.h, src/dense.c,
101 :     src/dgCMatrix.c, src/dsCMatrix.c, src/dtTMatrix.c, src/sparseQR.c,
102 :     src/t_gCMatrix_colSums.c: more R_CheckStack()s
103 :    
104 :     2007-07-05 18:12 Douglas Bates <bates@stat.wisc.edu>
105 :    
106 :     * [r4550] inst/include/Matrix.h: Add the macro N_AS_CHM_DN to "alloca"
107 :     the required amount of memory then call M_numeric_as_chm_dense.
108 :     * [r4556] src/Mutils.h, src/dgCMatrix.c: Define and use the Alloca macro
109 :     (like Calloc but calling alloca)
110 :    
111 : maechler 1947 2007-07-05 Martin Maechler <maechler@stat.math.ethz.ch>
112 :    
113 :     * R/sparseMatrix.R (printSpMatrix): renamed from prSpMatrix()
114 :     and extended with more sophisticated 'col.names' option.
115 :     * NAMESPACE: export printSparseMatrix()
116 :     * man/printSpMatrix.Rd: document, incl. examples
117 :    
118 : maechler 1960 2007-07-04 16:21 Douglas Bates <bates@stat.wisc.edu>
119 :    
120 :     * [r4543] src/cs_utils.c, src/cs_utils.h, src/dgCMatrix.c,
121 :     src/dtCMatrix.c, src/sparseQR.c: CSP typedef for *cs and macro
122 :     AS_CSP. API change - pass the empty structure to Matrix_as_cs.
123 :    
124 : maechler 1945 2007-07-04 Martin Maechler <maechler@stat.math.ethz.ch>
125 :    
126 :     * DESCRIPTION (Version): 0.99875-4
127 :    
128 :     * tests/Class+Meth.R (tstMatrixClass): add dimnames, and hence test
129 :     some dimnames perservation.
130 :    
131 :     * R/dsTMatrix.R (t-method): keep dimnames
132 :     * R/dtTMatrix.R: ditto
133 :    
134 :     * R/sparseMatrix.R (prSpMatrix): print colnames when non-trivial
135 :     and ncol(.) < 10
136 :    
137 :     * src/cs_utils.c: drop check_class() and use Matrix_check_class()
138 :     from Mutils.h
139 :    
140 :     * src/lgCMatrix.c ([ln]csc_to_matrix): no longer lose dimnames,
141 :     e.g. in as(<ngCMatrix>, "matrix")
142 :    
143 : maechler 1960 2007-07-01 13:27 Douglas Bates <bates@stat.wisc.edu>
144 :    
145 :     * [r4529] .: Create a branch for the API changes from the 0.99875
146 :     series to the 0.999375 series
147 :     * [r4530] DESCRIPTION, inst/include/Matrix.h,
148 :     inst/include/Matrix_stubs.c, src/CHMfactor.c, src/Csparse.c,
149 :     src/Mutils.h, src/Tsparse.c, src/chm_common.c, src/chm_common.h,
150 :     src/dense.c, src/dgCMatrix.c, src/dsCMatrix.c, src/dtTMatrix.c,
151 :     src/t_gCMatrix_colSums.c: API change - pass the empty structure to the
152 :     as_cholmod_x functions
153 :    
154 :     2007-06-30 09:05 Martin Maechler <maechler@stat.math.ethz.ch>
155 :    
156 :     * [r4527] trunk/Matrix/DESCRIPTION, trunk/Matrix/NAMESPACE,
157 :     trunk/Matrix/inst/doc/Comparisons.Rnw: add session- and hardware-info
158 :     to Comparisons
159 :    
160 :     >>>>>>> .merge-right.r4561
161 : maechler 1932 2007-06-29 Martin Maechler <maechler@stat.math.ethz.ch>
162 :    
163 :     * DESCRIPTION (Version): 0.99875-3 ready to be released.
164 :    
165 :     * R/sparseMatrix.R (spMatrix): make spMatrix(3,4) working
166 :    
167 :     * R/AllGeneric.R: set "Math" (and "Math2") group generics in a way
168 :     that should also work in a future version of R.
169 :    
170 : maechler 1922 2007-06-21 Martin Maechler <maechler@stat.math.ethz.ch>
171 :    
172 :     * NAMESPACE, R/AllClass.R: "xsparseVector" class union.
173 :    
174 :     * R/sparseVector.R: more *sparseVector coercions, notably for
175 :     non - double ones.
176 :    
177 : maechler 1911 2007-06-19 Martin Maechler <maechler@stat.math.ethz.ch>
178 :    
179 :     * R/colSums.R: new file for all (col|row)(Sums|Means) methods,
180 :     notably the new ones building on the new .Call(.)s:
181 :    
182 :     * src/dgCMatrix.c (DEF_gCMatrix_COLSUMS): use to define
183 :     all 4 of [dlin]gCMatrix_colSums().
184 :    
185 : bates 1909 2007-06-18 16:12 Douglas Bates <bates@stat.wisc.edu>
186 :    
187 :     * [r4472] src/Syms.h, src/init.c: Added Matrix_lengthSym
188 :     * [r4473] src/dgCMatrix.c: Modified dgCMatrix_colSums for sparseVector
189 :     result
190 : maechler 1911
191 : maechler 1903 2007-06-16 Martin Maechler <maechler@stat.math.ethz.ch>
192 :    
193 : maechler 1904 * R/kronecker.R: fix typo (could lead to inf.recursion)
194 :     * test/simple.R: testing that
195 :    
196 : maechler 1903 * R/sparseMatrix.R (prSpMatrix): change to be used as print()
197 : maechler 1922 method as well (which can have arguments, show() can't).
198 : maechler 1903
199 : bates 1902 2007-06-16 15:52 Douglas Bates <bates@stat.wisc.edu>
200 :    
201 :     * [r4466] R/dgCMatrix.R, src/dgCMatrix.c, src/dgCMatrix.h, src/init.c:
202 :     added dgCMatrix_colSums for [col,row][Sums,Means]
203 :    
204 : bates 1899 2007-06-15 23:15 Douglas Bates <bates@stat.wisc.edu>
205 : bates 1897
206 :     * [r4460] R/sparseMatrix.R, man/dgCMatrix-class.Rd, src/dgCMatrix.c,
207 :     src/dgCMatrix.h, src/init.c: added lm.fit.sparse (unexported),
208 :     coercion of "factor" to "dgCMatrix" and dgCMatrix_cholsol
209 :     * [r4461] R/AllClass.R, man/sparseMatrix-class.Rd: draft "indicators"
210 :     class
211 : bates 1899 * [r4463] R/sparseMatrix.R, man/dgCMatrix-class.Rd,
212 :     man/sparseMatrix-class.Rd: Don't need an "indicators" class - use the
213 :     row names to store the levels - duh! Added an example.
214 : maechler 1903
215 : maechler 1893 2007-06-14 Martin Maechler <maechler@stat.math.ethz.ch>
216 :    
217 :     * src/Csparse.c (Csparse_validate): check for *repeated* entries
218 :     thanks to example from Christian Buchta; with a test here:
219 :     * tests/simple.R:
220 :    
221 : maechler 1886 2007-06-07 Martin Maechler <maechler@stat.math.ethz.ch>
222 :    
223 :     * R/Auxiliaries.R (callGeneric): another fix, needed for some cases
224 :     of colSums(*, sparseResult = TRUE)
225 :    
226 : maechler 1883 2007-06-06 Martin Maechler <maechler@stat.math.ethz.ch>
227 :    
228 :     * R/lsparseMatrix.R, R/ldenseMatrix.R (all, any): change default to
229 :     'na.rm = FALSE' as "everywhere" else in R.
230 :    
231 : bates 1877 2007-06-05 Douglas Bates <bates@stat.wisc.edu>
232 :    
233 : bates 1878 * [r4421] src/CSparse_install.sh: Modify for new organization of
234 : maechler 1883 CSparse package
235 : bates 1877 * [r4425] src/UFsparse_download.sh: Update to version 3.0.0 of
236 :     SuiteSparse
237 :     * [r4426] src/Makefile: add ./UFconfig to the include path for
238 :     compilation
239 : maechler 1883 * [r4427] src/cs.[ch]: update to CSparse version 2.2.0
240 :     * [r4428] inst/doc/UFsparse/* src/{AMD,CHOLMOD,COLAMD}/*
241 :     src/UFconfig/UFconfig.h: Update to version 3.0.0 of SuiteSparse
242 :    
243 : maechler 1870 2007-06-05 Martin Maechler <maechler@stat.math.ethz.ch>
244 :    
245 :     * R/Auxiliaries.R (emptyColnames): + argument msg.if.not.empty, used in
246 :     * R/sparseMatrix.R (prSpMatrix): now gives a message about
247 :     suppressed column names.
248 :    
249 : bates 1868 2007-06-04 17:13 Douglas Bates <bates@stat.wisc.edu>
250 :    
251 :     * [r4418] src/Csparse.c, src/HBMM.c, src/Mutils.c, src/Mutils.h,
252 :     src/Tsparse.c, src/chm_common.c, src/chm_common.h, src/dgCMatrix.c,
253 :     src/dgeMatrix.c, src/dpoMatrix.c, src/dpoMatrix.h, src/dppMatrix.c,
254 :     src/dppMatrix.h, src/dsCMatrix.c, src/dspMatrix.c, src/dspMatrix.h,
255 :     src/dsyMatrix.c, src/dsyMatrix.h, src/dtpMatrix.c, src/dtrMatrix.c:
256 :     Remove warnings after change to const char* CHAR
257 :    
258 :     2007-06-04 17:11 Douglas Bates <bates@stat.wisc.edu>
259 :    
260 :     * [r4417] inst/include/Matrix_stubs.c, inst/include/cholmod.h: Corrected
261 :     type of M_cholmod_ssmult
262 :    
263 : bates 1863 2007-06-03 14:42 Douglas Bates <bates@stat.wisc.edu>
264 :    
265 :     * [r4412] inst/include/Matrix_stubs.c, inst/include/cholmod.h,
266 :     src/init.c: Yet another cholmod export - cholmod_ssmult
267 :    
268 : maechler 1855 2007-05-23 Martin Maechler <maechler@stat.math.ethz.ch>
269 :    
270 :     * NAMESPACE: exported drop0(), since
271 :     * man/drop0.Rd: I have seen several cases, I really wanted to use
272 :     it, so our users may want too.
273 :    
274 :     2007-05-22 Martin Maechler <maechler@stat.math.ethz.ch>
275 :    
276 :     * man/colSums.Rd: separately document colSums() etc, since these
277 :     have the extra argument 'sparseResult'.
278 :    
279 : maechler 1852 2007-05-21 Martin Maechler <maechler@stat.math.ethz.ch>
280 :    
281 :     * R/sparseMatrix.R (spMatrix): utility (T)sparse Matrix constructor;
282 :     * man/spMatrix.Rd: docu., including examples
283 :    
284 :     * R/Auxiliaries.R (sp.colMeans): etc, using a patched callGeneric(),
285 :     in order to make colMeans() etc fast *and* correct.
286 :     * R/sparseVector.R (replSPvec): "[<-" functionality for
287 :     sparseVectors; tested in
288 :     * tests/simple.R:
289 :    
290 :     2007-05-19 Martin Maechler <maechler@stat.math.ethz.ch>
291 :    
292 :     * R/sparseMatrix.R (print.sparseSummary): and summary() method for
293 :     (very) sparse Matrices; output similar to Matlab's print().
294 :    
295 : bates 1847 2007-05-17 Douglas Bates <bates@stat.wisc.edu>
296 :    
297 :     * src/HBMM.c (Matrix_writeMatrixMarket): Write 1-based, not
298 :     0-based, indices (Jose Quesada <quesada@gmail.com>).
299 :    
300 : bates 1844 2007-05-16 Douglas Bates <bates@stat.wisc.edu>
301 :    
302 :     * R/CHMfactor.R: Added solve methods for a CHMfactor object.
303 :    
304 : maechler 1845 2007-05-16 Martin Maechler <maechler@stat.math.ethz.ch>
305 :    
306 :     * R/Auxiliaries.R (sparsapply): new utility, much faster than
307 :     tapply1() for large sparse matrices.
308 :    
309 :     2007-05-15 Martin Maechler <maechler@stat.math.ethz.ch>
310 :    
311 :     * R/Matrix.R (dim<-): reshape now via sparseVector.
312 :    
313 :     * R/sparseVector.R: methods and function for
314 :     * R/AllClass.R: new "sparseVector" class and daughters.
315 :     * NAMESPACE: export new classes
316 :    
317 : maechler 1837 2007-05-14 Martin Maechler <maechler@stat.math.ethz.ch>
318 :    
319 :     * DESCRIPTION (Version): 0.99875-1
320 :     * src/Makefile.win: also remove Lapack code from here (cf. 04-25).
321 :    
322 : maechler 1834 2007-05-11 Martin Maechler <maechler@stat.math.ethz.ch>
323 :    
324 :     * R/Tsparse.R ([, Tsparse): fix last case: *duplicated*, symmetric
325 :     indexing
326 :     * tests/indexing.R: test set for that.
327 :    
328 : maechler 1833 2007-05-08 Martin Maechler <maechler@stat.math.ethz.ch>
329 :    
330 :     * R/Tsparse.R (replTmat): fix the case of *duplicated* index
331 :     entries.
332 :     * tests/indexing.R(out): add regression test for it
333 :    
334 :     2007-04-30 Martin Maechler <maechler@stat.math.ethz.ch>
335 :    
336 :     * R/(l(dense|sparse))?Matrix.R (!): use 'x', not 'e1' as argument
337 :     name for "!" method definitions.
338 :    
339 : maechler 1829 2007-04-26 Martin Maechler <maechler@stat.math.ethz.ch>
340 :    
341 :     * R/Tsparse.R (intI): new utility, used for "[" :
342 :     Cleanup up there, and fixes for duplicated indices - more TODO!
343 :    
344 :     * tests/indexing.R(out): more tests
345 :    
346 : bates 1827 2007-04-25 Douglas Bates <bates@stat.wisc.edu>
347 :    
348 :     * DESCRIPTION,src/Makefile: require R>= 2.5.0 and remove Lapack
349 :     code that is now part of the R Lapack library.
350 : maechler 1829
351 : bates 1827 * src/init.c,inst/include/{Matrix_stubs.c,cholmod.h}:export
352 :     cholmod_factorize_p (used in lme4 for GLMMs and NLMMs).
353 :    
354 : maechler 1829 2007-04-21 Martin Maechler <maechler@stat.math.ethz.ch>
355 :    
356 :     * R/Matrix.R (image): method for all Matrices, not just sparse ones.
357 :    
358 :     2007-04-17 Martin Maechler <maechler@stat.math.ethz.ch>
359 :    
360 :     * R/Auxiliaries.R (tapply1): unname(.) -> colSums() etc don't end
361 :     up with extraneous names '0'...'<n-1>'
362 :    
363 : maechler 1825 2007-04-12 Martin Maechler <maechler@stat.math.ethz.ch>
364 :    
365 :     * R/dgTMatrix.R (mat2dgT): care about NAs
366 :    
367 :     2007-04-11 Martin Maechler <maechler@stat.math.ethz.ch>
368 :    
369 :     * R/kronecker.R: triangularity preserving methods
370 :    
371 : maechler 1803 2007-03-27 Martin Maechler <maechler@stat.math.ethz.ch>
372 :    
373 :     * R/kronecker.R: new file collecting kronecker() methods in one
374 :     place. Goal: become much faster!
375 :    
376 : maechler 1799 2007-03-23 Martin Maechler <maechler@stat.math.ethz.ch>
377 :    
378 :     * src/dtCMatrix.c (dtCMatrix_solve): use the new code from Kasper
379 :     Kristensen based cs_spsolve() instead of _lsolve & _usolve which
380 :     can be much faster.
381 :    
382 :     * tests/matprod.R: add regression tests for these (upper & lower).
383 :    
384 :     2007-03-19 Martin Maechler <maechler@stat.math.ethz.ch>
385 :    
386 :     * R/Matrix.R (diff): method for our Matrices.
387 :    
388 :     * R/sparseMatrix.R (isDiagonal): check dim()!
389 :    
390 :     2007-03-17 Martin Maechler <maechler@stat.math.ethz.ch>
391 :    
392 :     * R/Matrix.R (dim<-): new method for "reshape()" built on a
393 :     proposal from Tamas Papp.
394 :    
395 :     2007-03-16 Martin Maechler <maechler@stat.math.ethz.ch>
396 :    
397 :     * R/AllGeneric.R: remove all if(!isGeneric(.)) clauses
398 :    
399 :     * R/zzz.R (.onLoad, .onUnload): do *not* leave bind_activation(TRUE);
400 : maechler 1803 rather define and export cBind() and rBind() only.
401 :     --> useRs *must* change code that used to have cbind()/rbind() !!
402 : maechler 1799
403 : maechler 1803 * R/bind.R: change tests from cbind() to cBind() and similarly to rBind()
404 :     * R/bind.Rout.save: ditto
405 : maechler 1799
406 : bates 1787 2007-02-16 Douglas Bates <bates@r-project.org>
407 :    
408 :     * DESCRIPTION (Date, Version): 0.9975-11 with new date
409 :     * src/dgCMatrix.c (R_to_CMatrix, compressed_to_TMatrix): remove
410 :     const modifier on declaration of the array 'valid'
411 :    
412 : bates 1786 2007-02-12 Douglas Bates <bates@stat.wisc.edu>
413 :    
414 :     * R/CHMfactor.R: Add image method (coercion to sparseMatrix).
415 :    
416 : maechler 1765 2007-02-05 Martin Maechler <maechler@stat.math.ethz.ch>
417 :    
418 : maechler 1768 * DESCRIPTION (Date, Version): 0.9975-10 with new date.
419 :    
420 : maechler 1767 * R/Ops.R (Arith): make sure Csparse o Csparse also works for e.g. ntCMatrix
421 :     * tests/simple.R: test the above and some of these coercions:
422 :    
423 :     * R/nsparseMatrix.R: coercing "Csparse" to "lsparseMatrix";
424 :     be careful to avoid infinite recursion, using new coercions in
425 :     * R/ngCMatrix.R and nsC... and ntC...
426 :     * R/lsparseMatrix.R: ditto
427 :    
428 : maechler 1765 * R/SparseM-conv.R: more conversion, notably for triplet matrices.
429 :    
430 : maechler 1767 * src/dgCMatrix.c (R_to_C_Matrix): port Doug's fix and
431 :     * R/Rsparse.R: reactivate .Call()s
432 : maechler 1765
433 : maechler 1767 * tests/Class+Meth.R: a bit more on actual classes
434 :    
435 :     2007-02-04 Douglas Bates <bates@stat.wisc.edu>
436 :    
437 :     * src/dgCMatrix.c (compressed_to_TMatrix): fix memory bug using strdup()
438 :    
439 : maechler 1760 2007-02-03 Martin Maechler <maechler@stat.math.ethz.ch>
440 : maechler 1758
441 :     * DESCRIPTION (Version): 0.9975-10 to upload
442 :    
443 : maechler 1760 * tests/Class+Meth.R (tstMatrixClass): require coercions to
444 :     specific classes less unconditionally.
445 :    
446 :     * R/Auxiliaries.R: get rid of as_Tsparse() and as_Rsparse()
447 :    
448 :     * R/Tsparse.R (triu): etc, use as(*, "TsparseMatrix") instead of as_Tsparse()
449 :    
450 :     * R/Rsparse.R (.R.2.T): R-level workaround using compressed_to_TMatrix.
451 : maechler 1758 * R/Rsparse.R (.R.2.C): R-level workaround since C-level
452 :     R_to_CMatrix segfaults on one platform.
453 : maechler 1760 Eliminate most coercion method to *specific* classes, and replace
454 :     with virtual classes coercions.
455 : maechler 1758
456 : maechler 1760
457 : maechler 1758 2007-02-01 Martin Maechler <maechler@stat.math.ethz.ch>
458 :    
459 :     * src/init.c: export the CHM...._validate() placeholders, since
460 :     they *are* called.
461 :    
462 : maechler 1760 * tests/Class+Meth.R (classCanCoerce): and starting to test
463 : maechler 1758 all as(<from>, <to>)
464 :    
465 : maechler 1751 2007-01-30 Martin Maechler <maechler@stat.math.ethz.ch>
466 :    
467 :     * R/Tsparse.R ([): more care when subsetting triangular Tsparse
468 :     * tests/indexing.R: tested now
469 :     * tests/indexing.Rout.save: updated
470 :    
471 :     * src/Csparse.c (Csparse_to_dense): use Rkind = -1 for PATTERN to
472 :     * src/chm_common.c (chm_dense_to_SEXP): return "ngeMatrix" when
473 :     appropriate.
474 :    
475 :     * NAMESPACE: export a trivial
476 :     * R/Matrix.R: drop() Matrix-method
477 :    
478 :     * R/AllClass.R: moved all prototypes to virtual super classes.
479 :    
480 :     * R/Rsparse.R: many more coercions to have less exceptions in
481 :     * tests/Class+Meth.R:
482 :    
483 :     * R/Ops.R (Compare): tweak for case with NA
484 :     * tests/simpl.R: hence another 'FIXME' eliminated
485 :    
486 : maechler 1747 2007-01-29 Martin Maechler <maechler@stat.math.ethz.ch>
487 :    
488 : maechler 1748 * R/diagMatrix.R (solve): the obvious methods for diagonalMatrix
489 :     objects.
490 :    
491 : maechler 1747 * tests/Class+Meth.R (tstMatrixClass): now testing diag(), nnzero(),
492 :     and more of "!", "&", "|", all, any; coercions
493 :    
494 :     * R/Rsparse.R: many coercions (which enable quite a few other
495 :     methods), thanks to enhancements in
496 :     * src/dgCMatrix.c (R_to_CMatrix): new, and
497 :     * src/dgCMatrix.c (compressed_to_TMatrix): now for (d,l,n) ,
498 :     symmetric & triangular and ..RMatrix objects.
499 :    
500 :     * src/TMatrix_as.c (Matrix_T_as_DENSE,Matrix_T_as_GENERAL):
501 :     renamed file from src/dsTMatrix.c;
502 :     now dealing with symmetric and triangular Tsparse coercions, both
503 :     to dense and general.
504 :    
505 :     2007-01-27 Martin Maechler <maechler@stat.math.ethz.ch>
506 :    
507 :     * src/dsTMatrix.c: has now "l" and "n" methods besides the "d" ones.
508 :    
509 :     * R/Ops.R (Arith): <dgCMatrix> o <numeric> now remains sparse
510 :     where sensible when the <numeric> is of length > 1.
511 :    
512 :     2007-01-26 Martin Maechler <maechler@stat.math.ethz.ch>
513 :    
514 :     * R/Matrix.R ([<-): for M[] <- value: fix length
515 :    
516 :     2007-01-25 Martin Maechler <maechler@stat.math.ethz.ch>
517 :    
518 :     * R/Auxiliaries.R (n2l_Matrix): new, to be used in
519 :     * R/ndenseMatrix.R: new coercions n* -> l*
520 :    
521 : maechler 1738 2007-01-22 Martin Maechler <maechler@stat.math.ethz.ch>
522 :    
523 :     * R/triangularMatrix.R: new file; simple triu() and tril() methods.
524 :    
525 :     * R/Ops.R ("Logic"): and other "Ops", many updates
526 :    
527 :     2007-01-18 Martin Maechler <maechler@stat.math.ethz.ch>
528 :    
529 :     * src/Mutils.h (SET_DimNames): new utility
530 :    
531 :     * R/Auxiliaries.R (nnzero): improved and now exported via
532 :    
533 :     * NAMESPACE: + nnzero(); length() == prod(dim(.)) method for all "Matrix" objects
534 :    
535 : maechler 1725 2007-01-17 Martin Maechler <maechler@stat.math.ethz.ch>
536 :    
537 :     * R/diagMatrix.R (!): fix typo.
538 :    
539 :     2007-01-16 Martin Maechler <maechler@stat.math.ethz.ch>
540 :    
541 :     * R/Auxiliaries.R (as_Csparse): and quite a few others:
542 :     allow to pass class definition --> speedup
543 :     * R/sparseMatrix.R: apply the above
544 :    
545 :     * R/Csparse.R: coercion Csparse* to dense* now preserves shape properties.
546 :    
547 :     * src/Mutils.h (mMatrix_as_geMatrix): new, based on
548 :     * src/Mutils.c (dup_mMatrix_as_geMatrix): new; generalization of
549 :     old dup_mMatrix_as_dgeMatrix), eliminating a long-standing "FIXME".
550 :    
551 :     * src/dense.c (dense_to_Csparse): use new mMatrix_as_geMatrix()
552 :    
553 :     * R/denseMatrix.R (.dense2C): based on dense_to_Csparse: name it,
554 :     and use it for "sparse*" as well, since it's faster than the
555 :     as_Csparse(.) way.
556 :    
557 :     2007-01-15 Martin Maechler <maechler@stat.math.ethz.ch>
558 :    
559 :     * R/Ops.R ("Logic"): more methods, notably an <lgC> o <lgC> one.
560 :    
561 : maechler 1724 2007-01-12 Martin Maechler <maechler@stat.math.ethz.ch>
562 :    
563 :     * R/Tsparse.R (.TM.repl.i.2col): new internal function to be used
564 :     as method for M[ ij ] <- v
565 :     * R/Csparse.R:: go via Tsparse for "M[ij] <- v"
566 :    
567 :     * R/Ops.R: "Compare" for (C|R)sparse: need pointer slot for all
568 :     FALSE answer
569 :    
570 :     * R/Csparse.R (replCmat): fix the "all non-zero" case with reordering
571 :     * tests/indexing.R: test it, and some of the above
572 :    
573 :     2007-01-05 Martin Maechler <maechler@stat.math.ethz.ch>
574 :    
575 :     * R/Auxiliaries.R (is_duplicatedT): new utility
576 :    
577 : bates 1716 2007-01-05 Douglas Bates <bates@stat.wisc.edu>
578 :    
579 :     * src/init.c (R_init_Matrix): export cholmod_scale
580 :    
581 : maechler 1724 2006-12-30 Martin Maechler <maechler@stat.math.ethz.ch>
582 :    
583 :     * R/zzz.R (tmp): for R >= 2.5.0, extend formals of our
584 :     base::as.matrix to (x, ...)
585 :    
586 : maechler 1714 2006-12-28 Martin Maechler <maechler@stat.math.ethz.ch>
587 :    
588 :     * R/Ops.R ("Arith" etc): move almost all "Ops" methods to new R
589 :     file; start using "Logic", hence
590 :    
591 :     * DESCRIPTION (Depends): R >= 2.4.1 (since we want "Logic")
592 :     * NAMESPACE: import and export "Logic"
593 :    
594 :     2006-12-27 Martin Maechler <maechler@stat.math.ethz.ch>
595 :    
596 :     * src/zpotfr.f and dependencies: use LAPACK 3.1 version
597 :     only needed previously to R version 2.5.0.
598 : maechler 1724
599 : maechler 1710 2006-12-26 Martin Maechler <maechler@stat.math.ethz.ch>
600 :    
601 :     * DESCRIPTION (Date, Version): 0.9975-8, ready for release
602 :    
603 :     * R/Tsparse.R (replTmat): fix subassignment of triangular
604 :     * R/Csparse.R (replCmat): ditto
605 :     * tests/indexing.R: more tests, incl the above fix
606 :    
607 :     2006-12-23 Martin Maechler <maechler@stat.math.ethz.ch>
608 :    
609 :     * R/Auxiliaries.R (drop0): extend for non CSparse
610 :     * R/Auxiliaries.R (diagU2N): should work for all sparseMatrix
611 :    
612 :     * src/Csparse.c (Csparse_to_Tsparse, Csparse_general_to_symmetric):
613 :     use uplo correctly (!); other places: use uplo_P() macro
614 :    
615 :     * R/Csparse.R (replCmat): call diagU2N() when needed
616 :     * R/Tsparse.R (replTmat): ditto
617 :    
618 :     * src/dtCMatrix.c (tCMatrix_validate): new
619 :     * src/dtTMatrix.c (tTMatrix_validate): new, used in
620 :     * R/AllClass.R: for validity of dtC, dsC, and dtT, dsT.
621 :    
622 :     * R/diagMatrix.R (replDiag): to use in [<-
623 :    
624 : maechler 1708 2006-12-22 Martin Maechler <maechler@stat.math.ethz.ch>
625 :    
626 :     * R/Auxiliaries.R (as_Csparse2, as_geSimpl): new functions;
627 :     also more general diagU2N().
628 :    
629 :     2006-12-21 Martin Maechler <maechler@stat.math.ethz.ch>
630 :    
631 :     * R/bind2.R: new file for all cbind2(), rbind() methods moved here
632 :     from R/<foo>Matrix.R files. Better diagonal & improved sparse methods.
633 :    
634 : maechler 1707 2006-12-20 Martin Maechler <maechler@stat.math.ethz.ch>
635 :    
636 :     * tests/bind.R: a few more cases
637 :     * R/Auxiliaries.R (.M.kind): also work for atomic vectors
638 :    
639 :     * R/denseMatrix.R (cbind2/rbind2): moved here (and generalized) from
640 :     * R/ddenseMatrix.R (cbind2/rbind2)
641 :     * R/Tsparse.R (replTmat): final(?!) fix for "[<-" ..
642 :     * tests/indexing.R
643 :     * tests/indexing.Rout.save: updated
644 :    
645 :     2006-12-18 Martin Maechler <maechler@stat.math.ethz.ch>
646 :    
647 :     * R/Tsparse.R (replTmat): fixed a remaining "[<-" bug in
648 :     * tests/indexing.R
649 :    
650 : maechler 1705 2006-12-15 Martin Maechler <maechler@stat.math.ethz.ch>
651 :    
652 :     * R/sparseMatrix.R (prSpMatrix): "." alignment much improved:
653 :     align with proper position of "0", i.e., right for integers.
654 :     argument 'align' by default is "fancy".
655 :    
656 :     2006-12-14 Martin Maechler <maechler@stat.math.ethz.ch>
657 :    
658 :     * R/sparseMatrix.R: delegate "Compare" to "Csparse.."
659 :     * R/Csparse.R: and fix "Compare" for more cases.
660 :     * tests/Class+Meth.R: test some of these (m == m, m != m)
661 :    
662 :     2006-12-13 Martin Maechler <maechler@stat.math.ethz.ch>
663 :    
664 :     * R/lsparseMatrix.R: all() and any() methods
665 :     * R/ldenseMatrix.R: ditto
666 :     * NAMESPACE, R/Matrix.R: ditto
667 :    
668 :     * man/all-methods.Rd: document them minimally
669 :    
670 :     * tests/simple.R: add a few examples for these
671 :    
672 : maechler 1696 2006-12-11 Martin Maechler <maechler@stat.math.ethz.ch>
673 :    
674 :     * R/Tsparse.R ([): fix long standing typo in symmetric case
675 :     * man/dsCMatrix-class.Rd: add example exhibiting the above case
676 :    
677 : bates 1691 2006-12-10 Douglas Bates <bates@stat.wisc.edu>
678 :    
679 :     * src/CHMfactor.c (CHMfactor_to_sparse): change LDL factorization
680 :     to LL before converting to a sparse matrix. (The LDL form can be
681 :     converted to a sparse matrix but it is implicitly a unit
682 :     triangular matrix and a diagonal matrix overwritten on the diagonal.)
683 :    
684 :     2006-12-09 Douglas Bates <bates@stat.wisc.edu>
685 :    
686 :     * src/chm_common.c (chm_factor_to_SEXP): allocate and fill the Dim slot.
687 :    
688 : bates 1688 2006-12-08 Douglas Bates <bates@stat.wisc.edu>
689 :    
690 :     * DESCRIPTION (Version): updated -> release 0.9975-7
691 :     * src/{init.c,chm_common.c}, inst/include/*: export cholmod_analyze_p
692 :    
693 : maechler 1682 2006-11-30 Martin Maechler <maechler@stat.math.ethz.ch>
694 :    
695 :     * R/diagMatrix.R (%*%): write a direct [diag o Csparse] method
696 :    
697 : bates 1681 2006-11-29 Douglas Bates <bates@stat.wisc.edu>
698 :    
699 :     * src/dgeMatrix.c (dgeMatrix_solve): Check error code from dgetri.
700 :     * tests/dg_Matrix.R: Add Barry Rowlingson's test of a matrix that
701 :     is exactly singular.
702 :    
703 : maechler 1674 2006-11-07 Martin Maechler <maechler@stat.math.ethz.ch>
704 :    
705 :     * DESCRIPTION (Date): updated -> release 0.9975-6
706 :    
707 : maechler 1673 2006-11-06 Martin Maechler <maechler@stat.math.ethz.ch>
708 :    
709 :     * R/Csparse.R (replCmat): symmetric indexing of symmetric matrix
710 :     now returns symmetric.
711 :    
712 :     * R/zzz.R ("diag<-"): replace "diag<-" in base for R <= 2.4.x
713 :    
714 :     * R/Matrix.R (.M.sub.i.2col): new, for M[ cbind(i,j) ] indexing.
715 :     * R/Matrix.R (.M.repl.i.2col): new, for M[ cbind(i,j) ] <- value
716 :    
717 :     * R/Auxiliaries.R (.type.kind): added
718 :    
719 :     2006-11-04 Martin Maechler <maechler@stat.math.ethz.ch>
720 :    
721 :     * src/cs.[ch]: updated to CSparse Version 2.0.3 by simply
722 :     running src/CSparse_install.sh
723 :    
724 :     * R/denseMatrix.R: "[": keep symmetric on symmetric indexing.
725 :    
726 : maechler 1665 2006-11-03 Martin Maechler <maechler@stat.math.ethz.ch>
727 :    
728 :     * src/dsCMatrix.c (dsCMatrix_Csparse_solve): new
729 :     * R/dsCMatrix.R (solve): "fully-sparse" using the above.
730 :    
731 :     * R/AllClass.R: "pMatrix" now also inherits from "generalMatrix"
732 :    
733 :     * tests/Class+Meth.R (tstMatrixClass): now assure
734 :     the (important in method programming) property :
735 :    
736 :     ###>> Every "Matrix" is either
737 :     ###>> "general*", "symmetric*", "triangular*" or "diagonal*"
738 :    
739 :     (where "*" stands for "Matrix")
740 :    
741 :     * R/Auxiliaries.R (diagU2N): now .Call()s Csparse_diagU2N for <Csparse>
742 :    
743 :     * R/dMatrix.R (Compare(<dMatrix>,<dMatrix>): update and
744 :     * tests/validObj.R: checks for "comparison"
745 :    
746 :     * R/sparseMatrix.R ([): improved indexing for sparse;
747 :     trying to keep <symmetric>[ n, n] symmmetric
748 :    
749 :     * tests/indexing.R: indexing for logical sparse now ok
750 :    
751 :    
752 : maechler 1660 2006-11-02 Martin Maechler <maechler@stat.math.ethz.ch>
753 :    
754 : maechler 1661 * src/Tsparse.c: use xTsparse_validate() , and hence remove
755 :    
756 :     * src/{ltC,lsC,lgT}Matrix.[ch]: removed
757 :    
758 :     2006-11-02 Martin Maechler <maechler@stat.math.ethz.ch>
759 :    
760 : maechler 1660 * R/AllClass.R (Matrix-class): check length of dimnames in validity.
761 :    
762 :     * tests/simple.R: validObject() checking the above.
763 :    
764 : maechler 1665 * src/dgCMatrix.c (xCMatrix_validate): new, small and simple,
765 : maechler 1660 replacing both dgCMatrix_validate and lgCM*.
766 :    
767 :     * src/Csparse.c (Csparse_dense_prod, etc): do not lose dimnames;
768 :     fix dimnames setting in other places.
769 :     * src/chm_common.c (chm_dense_to_SEXP): now can pass dimnames
770 :    
771 : maechler 1659 2006-11-01 Martin Maechler <maechler@stat.math.ethz.ch>
772 :    
773 : maechler 1660 * R/Csparse.R,src/Csparse.c, etc: tcrossprod(<CsparseM>,<CsparseM>)
774 :    
775 :     * R/sparseMatrix.R (isSymmetric): drop 'factors' slot for
776 :     symmetry test, via
777 : maechler 1659 * R/Auxiliaries.R (.as.dgC.0.factors):
778 :    
779 : bates 1657 2006-11-01 Douglas Bates <bates@r-project.org>
780 :    
781 :     * R/Csparse.R,src/Csparse.c,tests/matprod.R,
782 :     man/CsparseMatrix-class.Rd: crossprod(<CsparseMatrix>,
783 :     <CsparseMatrix>) added
784 :    
785 : maechler 1655 2006-10-30 Martin Maechler <maechler@stat.math.ethz.ch>
786 :    
787 :     * tests/matprod.R: add a variation of Harri's example
788 :    
789 :     * R/dsparseMatrix.R: fix crossprod(<dsparse>, <dge>) to *not*
790 :     recursive infinitely.
791 :    
792 :     * R/dgCMatrix.R: + solve(<sparse>, <sparse>)
793 :    
794 :     * tests/indexing.R: add test for the "<" bug fixed 10-27 in R/dMatrix.R
795 :    
796 :     2006-10-28 Martin Maechler <maechler@stat.math.ethz.ch>
797 :    
798 :     * tests/Class+Meth.R (tstMatrixClass): more: use non-trivial
799 :     matrix if possible; test m+m == 2*m; now test dgRMatrix.
800 :     * R/dgRMatrix.R (.to.dgR): a few more coercions, in order to
801 :     satisfy the above test.
802 :    
803 : maechler 1654 2006-10-27 Martin Maechler <maechler@stat.math.ethz.ch>
804 :    
805 : maechler 1655 * R/Matrix.R (Ops): <Matrix> o <matrix> method added
806 :    
807 : maechler 1654 * R/dgCMatrix.R: solve(a, b="missing") based on
808 :     * src/dgCMatrix.c (dgCMatrix_matrix_solve): extend to work with
809 :     RHS = NULL.
810 :    
811 :     * R/diagMatrix.R (diagdiagprod): extend %*% etc to ldiMatrix;
812 :     add more (needed) [t]crossprod() methods.
813 :    
814 :     * man/ddiMatrix-class.Rd: more info, notably on 'diag'
815 :    
816 :     * R/Auxiliaries.R (as_CspClass): cleanup
817 :     (drop0): internal utility for "Csparse_drop(*, 0)"
818 :     (.bail.out.2): encourage active feedback
819 :    
820 :     2006-10-26 Martin Maechler <maechler@stat.math.ethz.ch>
821 :    
822 :     * R/dMatrix.R(Compare): new(), then slots [no validity check]
823 :    
824 :     * src/Csparse.c (Csparse_validate): fixed (and more efficient in
825 :     non-valid or 'sorted' case).
826 :    
827 :     * R/dsparseMatrix.R: add "chol" method.
828 :     * R/ddenseMatrix.R: ditto
829 :    
830 :     * R/diagMatrix.R (Ops): group methods for <diagonal> o <sparse>
831 :     * NAMESPACE (Ops)
832 :     * R/diagMatrix.R (diag2T): simple utility used "higher level"
833 :     coercion; deprecating direct lower level coercions.
834 :    
835 :     * R/*.R (seq): use seq_len() and seq_along() where possible.
836 :    
837 :    
838 : maechler 1647 2006-10-23 Martin Maechler <maechler@stat.math.ethz.ch>
839 :    
840 :     * DESCRIPTION (Version): 0.9975-5 ready for release
841 :    
842 : bates 1646 2006-10-20 Douglas Bates <bates@stat.wisc.edu>
843 :    
844 :     * src/init.c (R_init_Matrix): export more cholmod CCallable functions.
845 :    
846 : maechler 1642 2006-10-20 Martin Maechler <maechler@stat.math.ethz.ch>
847 :    
848 :     * R/AllClass.R (corMatrix): add 'validity' check;
849 :     comment out unused "LDL" class definition
850 :     * NAMESPACE: mention, but do not export "LDL" class
851 :     * R/corMatrix.R: new (simple), needed for R-devel with
852 :     * tests/Class+Meth.R (tstMatrixClass): 1 exception for corMatrix
853 :     coerce and t() exceptions for all 5 'Mat.MatFact' classes.
854 :    
855 : bates 1641 2006-10-19 Douglas Bates <bates@stat.wisc.edu>
856 :    
857 :     * src/chm_common.h: Add R_cholmod_start to initialize cholmod to
858 :     use Rprintf and R's error handling.
859 :    
860 : maechler 1635 2006-10-17 Martin Maechler <maechler@stat.math.ethz.ch>
861 :    
862 :     * R/diagMatrix.R (%*%): rep(*, each = .) in Matrix %*% diagonal.
863 :     * tests/matprod.R: add tests for the bug fixed.
864 :    
865 : bates 1624 2006-10-11 Douglas Bates <bates@stat.wisc.edu>
866 :    
867 :     * src/HBMM.[ch]: remove HarwellBoeing format for writing.
868 :     * src/SOURCES_C.mkf (SOURCES_C): no longer compile iohb.c
869 :    
870 :     2006-10-06 Douglas Bates <bates@stat.wisc.edu>
871 :    
872 : bates 1629 * R/d[gs]CMatrix.R: deprecate the writeHB function. Use writeMM instead.
873 : bates 1624
874 : maechler 1618 2006-10-06 Martin Maechler <maechler@stat.math.ethz.ch>
875 :    
876 :     * DESCRIPTION (Version): 0.9975-3
877 :    
878 :     * R/diagMatrix.R (bdiag): new function constructing block diagonal
879 :     (sparse) matrices.
880 :     * man/bdiag.Rd: docu + examples
881 :    
882 : maechler 1619 * R/Csparse.R (replCmat): calling new Csparse_drop() now.
883 :    
884 : maechler 1618 * src/Csparse.c (Csparse_general_to_symmetric, Csparse_drop): new functions
885 :     * R/lsCMatrix.R: three more coercions to lsC (thanks to the above)
886 :    
887 :     * R/diagMatrix.R (Diagonal): '[<-' method for diag.matrices such
888 :     that result is sparse or diagonal (and not dense).
889 :    
890 :     * man/Subassign-methods.Rd: fix examples
891 :    
892 :     * R/Matrix.R (Matrix): Matrix(0, *) or Matrix(*, sparse=TRUE)
893 :     should always return a sparse (and not sometimes a diagonal) matrix.
894 :    
895 : maechler 1615 2006-10-05 Martin Maechler <maechler@stat.math.ethz.ch>
896 :    
897 :     * R/Matrix.R ([<-): also for value "Matrix" or "matrix"
898 :    
899 : bates 1613 2006-10-04 Douglas Bates <bates@stat.wisc.edu>
900 :    
901 :     * DESCRIPTION (Version): 0.9975-2
902 : maechler 1615
903 : bates 1613 * inst/include/Matrix_stubs.c (M_cholmod_sparse_to_triplet): export more symbols
904 :    
905 : bates 1611 2006-10-02 Douglas Bates <bates@R-project.org>
906 :    
907 :     * tests/dg_Matrix.R: Simplify test taking into account new code.
908 :    
909 : maechler 1599 2006-09-29 Martin Maechler <maechler@stat.math.ethz.ch>
910 :    
911 : maechler 1600 * R/Csparse.R (replCmat): improve for missing i / j in non-simple cases
912 :    
913 : maechler 1599 * R/lsTMatrix.R: new files w/ missing methods
914 :     * R/nsTMatrix.R: " 'for completeness'
915 :    
916 :     * tests/Class+Meth.R: a bit less 'not.ok.classes'
917 :    
918 :     * R/Tsparse.R (t): generalized "t" method from "dgT*" to "Tsparse*"
919 :    
920 :    
921 : bates 1595 2006-09-28 Douglas Bates <bates@R-project.org>
922 :    
923 :     * src/dppMatrix.h: Ensure definition of dspMatrix_validate is
924 :     included.
925 :    
926 :     * src/init.c, inst/include/{Matrix.h,Matrix_stubs.h,cholmod.h}:
927 :     Export C-callable functions used in Zt_create in lme4.
928 :    
929 : maechler 1592 2006-09-28 Martin Maechler <maechler@stat.math.ethz.ch>
930 :    
931 :     * DESCRIPTION (Version): 0.9975-1
932 :    
933 :     * tests/simple.R: less checks fail; using NA, found that our
934 :     kronecker() is not base-compatible with NA's.
935 :    
936 :     * R/dMatrix.R: "Compare" method now implemented for all cases
937 :    
938 :     * R/Auxiliaries.R (indTri): == which([lower/upper].tri( * )) new utility
939 :    
940 :     * man/dtpMatrix-class.Rd: mention length of 'x' slot
941 :    
942 :     * src/dtpMatrix.c (dtpMatrix_validate): fix check
943 :     * src/dspMatrix.c (dspMatrix_validate): ditto
944 :    
945 :     * R/dtTMatrix.R (gt2tT): fix ("l" -> "n")
946 :     including coercion to [nl]tTMatrix.
947 :    
948 :     * R/diagMatrix.R (show): print a header line as for other classes.
949 :    
950 :     2006-09-27 Martin Maechler <maechler@stat.math.ethz.ch>
951 :    
952 :     * src/Makefile.win (SUBDIRS): fix typo
953 :    
954 : maechler 1583 2006-09-19 Martin Maechler <maechler@stat.math.ethz.ch>
955 :    
956 :     * DESCRIPTION (Date): ready to release 0.9975-0 to CRAN
957 :    
958 : bates 1577 2006-09-18 Douglas Bates <bates@stat.wisc.edu>
959 :    
960 :     * R/[CT]sparse.R (crossprod and tcrossprod): Handle the cases for x
961 :     symmetric and y missing in R code using %*% (cholmod_aat doesn't
962 :     accept a symmetric matrix).
963 :     * tests/group-methods.R: Uncomment test of crossprod applied to
964 :     lsCMatrix objects.
965 :    
966 : maechler 1575 2006-09-18 Martin Maechler <maechler@stat.math.ethz.ch>
967 :    
968 :     * R/AllClass.R (symmetricMatrix): add validity method (available
969 :     in C for a long time). Many "n..Matrix": drop (wrong) validity arg.
970 :    
971 :     * src/lgCMatrix.c (lgCMatrix_validate): check 'x' slot (!)
972 :    
973 :     * tests/indexing.Rout.save:
974 :     * tests/indexing.R: additions, mainly for 'lsparse'
975 :    
976 :     * R/diagMatrix.R (Diagonal) & coercion to lgTMatrix: fixes for NA
977 :     case.
978 :    
979 :     * R/Auxiliaries.R (nz.NA): new utility now used in nnzero()
980 :    
981 : maechler 1571 2006-09-16 Martin Maechler <maechler@stat.math.ethz.ch>
982 :    
983 : maechler 1572 * R/sparseMatrix.R (prSpMatrix): print logical NAs "visibly"
984 :     as 'N' (1-letter - Ok?)
985 :    
986 : maechler 1571 * tests/group-methods.R: add test for logical + NAs
987 :    
988 :     * R/dMatrix.R ("Compare"): fix to work with NA's
989 :    
990 :     * R/AllClass.R: "Cholesky" etc now inherit from MatrixFactorization.
991 :    
992 :     * src/lgCMatrix.c (ncsc_to_matrix): renamed from lcsc_to_matrix()
993 :     which is implemented.
994 :    
995 : maechler 1565 2006-09-15 Martin Maechler <maechler@stat.math.ethz.ch>
996 :    
997 : maechler 1571 * src/chm_common.c: coerce logical <-> double instead of
998 :     typecasting; needed for "l" matrix handling in cholmod.
999 : maechler 1565
1000 : maechler 1571 * tests/other-pkgs.R (graph): small extension in "graph" checks.
1001 :    
1002 : maechler 1565 * R/sparseMatrix.R (graphNEL -> Tsparse): method for weight case.
1003 :     (Tsp2grNEL): other fixes needed
1004 :    
1005 : maechler 1548 2006-09-11 Martin Maechler <maechler@stat.math.ethz.ch>
1006 :    
1007 :     * R/AllClass.R ("nMatrix"): and subclasses for "nonzero pattern"
1008 :     Matrices, since "lMatrix", also "lsparseM" can have NA
1009 :     * R/ndenseMatrix.R, etc: new source files
1010 :     * man/nsparseMatrix-classes.Rd, etc: new help files
1011 :     * tests/: adaptions
1012 :     * src/chm_common.c (chm_dense_to_SEXP): and others:
1013 :     new 'Rkind' argument: "l*" and "d*" both use CHOLMOD_REAL
1014 : maechler 1582 * src/Csparse.c, etc: ditto
1015 : maechler 1548
1016 : bates 1546 2006-09-11 Douglas Bates <bates@R-project.org>
1017 :    
1018 :     * src/Mutils.[ch],init.c inst/include/*.h: Move the
1019 :     alloc_d**Matrix functions to the lme4 package.
1020 :    
1021 : bates 1543 2006-09-09 Douglas Bates <bates@R-project.org>
1022 :    
1023 :     * src/dsCMatrix.c (dsCMatrix_Cholesky): igoring LDL = FALSE now
1024 : maechler 1544 fixed
1025 : bates 1543
1026 : maechler 1544 2006-09-09 Martin Maechler <maechler@stat.math.ethz.ch>
1027 :    
1028 : maechler 1548 * R/lMatrix.R: new
1029 :    
1030 : maechler 1544 * R/sparseMatrix.R (Tsp2grNEL): do not yet use graph::foo()
1031 :    
1032 :     * R/dgeMatrix.R: do not define tcrossprod() methods for "matrix"
1033 : maechler 1582 * man/tcrossprod.Rd: ditto
1034 : maechler 1544
1035 : bates 1538 2006-09-08 Douglas Bates <bates@stat.wisc.edu>
1036 :    
1037 :     * inst/include/Matrix_stubs.c,Matrix.h: Add declarations and stubs
1038 :     for exported functions
1039 :     * src/Makefile, src/CHOLMOD/Lib/Makefile, src/Metis,CAMD,CCOLAMD:
1040 :     Remove partitioning algorithms for sparse matrix reordering. The
1041 :     copyright on the Metis code was problematic and the methods were
1042 :     rarely used.
1043 :     * src/triplet_to_col.[ch],MMHB.[ch]: Remove triplet_to_col. Such
1044 :     operations are now done entirely in CHOLMOD code.
1045 :    
1046 : bates 1517 2006-09-06 Douglas Bates <bates@R-project.org>
1047 :    
1048 :     * src/Mutils.h: Remove functions that are no longer used.
1049 :    
1050 : bates 1507 2006-09-04 Douglas Bates <bates@R-project.org>
1051 :    
1052 :     * src/dtCMatrix.c (dtCMatrix_validate): rename functions.
1053 :     * src/DEPS.mkf: update
1054 :    
1055 : maechler 1481 2006-09-02 Martin Maechler <maechler@stat.math.ethz.ch>
1056 :    
1057 :     * created branches/Matrix-for-R-2.3.x; on trunk: do
1058 :     * DESCRIPTION (Version): 0.9975-0
1059 :     (Depends): R (>= 2.4.0)
1060 :    
1061 : bates 1475 2006-09-01 Douglas Bates <bates@R-project.org>
1062 :    
1063 :     * R/sparseMatrix.R: Added direct method to CsparseMatrix from graphNEL
1064 :    
1065 : maechler 1472 2006-09-01 Martin Maechler <maechler@stat.math.ethz.ch>
1066 :    
1067 :     * R/sparseMatrix.R: add coercion from "ANY" to "sparseMatrix"
1068 :     * R/denseMatrix.R: add coercion from "ANY" to "denseMatrix"
1069 :    
1070 :     * R/Matrix.R ([): use nargs() to disambiguate M[i] and M[i,]
1071 :    
1072 :     2006-08-31 Martin Maechler <maechler@stat.math.ethz.ch>
1073 :    
1074 :     * R/sparseMatrix.R (Arith): moved Arith group method one-level up
1075 :     from "dsparse" to "sparse" and now go via "Csparse" instead of "dgC"
1076 : maechler 1582 * R/dsparseMatrix.R: ditto
1077 :     * R/Csparse.R: ditto
1078 : maechler 1472
1079 :     2006-08-31 Martin Maechler <maechler@stat.math.ethz.ch>
1080 :    
1081 :     * R/dMatrix.R (Compare): improve availability of "<", etc
1082 :     * R/Auxiliaries.R (asTuniq): new; also make use of R 2.4.x print(*,max)
1083 :    
1084 : maechler 1467 2006-08-30 Martin Maechler <maechler@stat.math.ethz.ch>
1085 :    
1086 :     * R/dgCMatrix.R: aargh: "Arith(<dgC>, numeric)" was wrong because
1087 :     of a 0-index which was used as 1-index (..hmm)
1088 :    
1089 :     * R/sparseMatrix.R (prSpMatrix): fix printing an all-0 sparse Matrix
1090 :    
1091 :     * R/Auxiliaries.R (all0, is0): for 0-testing in presence of NA's
1092 :     * R/Auxiliaries.R (isTriMat): use all0() for 0-testing.
1093 : maechler 1582 (.is.diagonal): ditto
1094 : maechler 1467
1095 :     * R/lgTMatrix.R: as("matrix", "lgTMatrix"): warn about NA's
1096 :    
1097 :     * R/Matrix.R (Matrix): also work for NA data
1098 :    
1099 : maechler 1455 2006-08-28 Martin Maechler <maechler@stat.math.ethz.ch>
1100 :    
1101 :     * R/Matrix.R (Matrix): + 'forceCheck' argument; dimnames setting
1102 :     in all cases.
1103 :    
1104 : bates 1453 2006-08-27 Douglas Bates <bates@R-project.org>
1105 :    
1106 :     * src/dense.[ch],init.c, R/ddenseMatrix.R, man/band.Rd
1107 :     (ddense_band): Added triu, tril and band for ddenseMatrix objects.
1108 :    
1109 : maechler 1447 2006-08-25 Martin Maechler <maechler@stat.math.ethz.ch>
1110 :    
1111 :     * src/Mutils.c (dup_mMatrix_as_dgeMatrix): added all subclasses of
1112 :     subclasses of "ddenseMatrix"
1113 :     * src/init.c et al: outcomment dtrM*_as_dge* and dsyM*_as_dge*_
1114 :     * R/ddenseMatrix.R et al: setAs("ddenseMatrix", "dgeMatrix", ..)
1115 :     instead of half dozen specialized ones.
1116 :    
1117 : bates 1445 2006-08-25 Douglas Bates <bates@R-project.org>
1118 :    
1119 :     * R/lmer.R (qqmath method): Bug fix provided by Emmanuel Tillard
1120 :     <tillard@cirad.fr> - ordering standard errors to match effects.
1121 :    
1122 : bates 1439 2006-08-24 Douglas Bates <bates@R-project.org>
1123 : bates 1431
1124 : bates 1439 * src/lsCMatrix.c (lsCMatrix_trans): Remove lsCMatrix_chol based
1125 :     on R_ldl.
1126 :     * R/lCholCMatrix.R,
1127 :     src/[dl]CholCMatrix.[ch],R_ldl.[ch],Metis_utils.[ch]: removed
1128 :     * src/dsCMatrix.c (dsCMatrix_to_dgTMatrix): use CHOLMOD
1129 :     * many files in ./R and ./src: Use more general version of
1130 :     dup_mMatrix_as_dgeMatrix to simplify method definitions.
1131 : bates 1442 * src/Mutils.c (dup_mMatrix_as_dgeMatrix): Add ddiMatrix,
1132 :     dtpMatrix, dspMatrix and dppMatrix conversions.
1133 :    
1134 : maechler 1447
1135 : bates 1439 2006-08-23 Douglas Bates <bates@R-project.org>
1136 :    
1137 :     * R/AllClass.R,lCholCMatrix.R,src/SOURCES_C.mkf,init.c,NAMESPACE:
1138 :     Remove classes lCholCMatrix and dCholCMatrix based on R_ldl code.
1139 : bates 1431 * src/dgeMatrix.c: Ensure 'factors' slot exists in result of
1140 :     dgeMatrix_crossprod (may need to do this in other places).
1141 :     * R/AllGeneric.R,dsCMatrix.R, src/dscMatrix.[ch]: Add Cholesky
1142 :     generic and method for dsCMatrix. Use CHOLMOD for chol().
1143 :    
1144 : bates 1414 2006-08-22 Douglas Bates <bates@R-project.org>
1145 :    
1146 :     * src/Mutils.c (dup_mMatrix_as_dgeMatrix): updated for general
1147 :     types of classed Matrices, matrices or numeric or logical vectors.
1148 : bates 1423 * src/init.c: register dup_mMatrix_as_dgeMatrix for coercions.
1149 :     * src/chm_common.c,Mutils.h (as_cholmod_factor): Move check_class
1150 :     to Mutils.h (as an inline) and change name to Matrix_check_class;
1151 :     fixes in as_cholmod_factor and chm_factor_to_SEXP.
1152 :     * src/dsCMatrix.[ch]: Use CHOLMOD for dsCMatrix_chol and
1153 :     dsCMatrix_matrix_solve. Comment out vestigial functions.
1154 :     * src/Csparse.c: use diag_P and uplo_P macros.
1155 : maechler 1447
1156 : bates 1405 2006-08-21 Douglas Bates <bates@R-project.org>
1157 :    
1158 :     * src/lmer.c (internal_mer_RZXinv): Fix memory leak caught by
1159 : maechler 1447 valgrind.
1160 : bates 1411 * tests/matprod.R: Add tests to verify that 'solve' and '%*%' are
1161 :     inverses.
1162 :     * src/sparseQR.c (sparseQR_validate): add new validation test, fix
1163 :     -Wall warnings.
1164 :     * src/dppMatrix.c,dtrMatrix.c,dgCMatrix.c,dgeMatrix.c,dspMatrix.c:
1165 :     Use dup_mMatrix_as_dgeMatrix.
1166 : maechler 1447
1167 : bates 1403 2006-08-20 Douglas Bates <bates@R-project.org>
1168 :    
1169 :     * src/sparseQR.c: Fix thinko in sparseQR_resid_fitted.
1170 :     * tests/sparseQR.R: Added
1171 :     * man/sparseQR-class.Rd: Document methods for qr.* generics
1172 :     * R/sparseQR.R: Return correct # of coefs; fix cut-and-paste errors
1173 :    
1174 : bates 1398 2006-08-19 Douglas Bates <bates@R-project.org>
1175 :    
1176 :     * NAMESPACE, R/sparseQR.R, src/init.c,sparseQR.[ch],SOURCES_C.mkf:
1177 :     Added methods for sparseQR for qr.qy, qr.qty, qr.coef, qr.resid
1178 :     and qr.fitted.
1179 :     * src/Mutils.[ch]: Added dup_mMatrix_as_dgeMatrix utility
1180 :     * src/dgCMatrix.c: Check for ordering before storing q in dgCMatrix_QR
1181 :    
1182 : maechler 1389 2006-08-18 Martin Maechler <maechler@stat.math.ethz.ch>
1183 :    
1184 :     * R/AllGeneric.R: add "qr" and "chol" generics; via 'trick' since
1185 :     the base version has no "..." argument.
1186 :    
1187 :     * R/sparseMatrix.R (prSpMatrix): fix the triangular unit diagonal case.
1188 :    
1189 :     * R/Matrix.R: define and
1190 :     * NAMESPACE: export as.numeric() and as.logical() methods.
1191 :     Let's hope these do not badly slow down something...
1192 :     Finally export the zapsmall() method.
1193 :    
1194 : bates 1388 2006-08-17 Douglas Bates <bates@R-project.org>
1195 :    
1196 :     * src/dgCMatrix.[ch] (dgCMatrix_matrix_solve), src/init.c,
1197 :     R/dgCMatrix.R: solve methods for dgCMatrix and dense RHS.
1198 :     * src/dtCMatrix.c :Remove code that is no longer used
1199 :     * R/dtCMatrix.R: Use C code for diagU2N in CsparseMatrix classes
1200 :    
1201 : bates 1370 2006-08-14 Douglas Bates <bates@R-project.org>
1202 :    
1203 : bates 1373 * src/Csparse.[ch],init.c (Csparse_to_logical): Added utilities
1204 :     Csparse_to_logical and Csparse_symmetric_to_general.
1205 :     * R/dgCMatrix.R,dsCMatrix.R,Csparse.R : Consolidate general
1206 : maechler 1389 coercion methods between CsparseMatrix and TsparseMatrix.
1207 : bates 1373
1208 :     2006-08-14 Douglas Bates <bates@R-project.org>
1209 :    
1210 : bates 1370 * R/dtCMatrix.R,dgCMatrix.R,Csparse.R src/init.c,dgCMatrix.[ch],
1211 :     Csparse.[ch],chm_common.c,dense.c : Use CHOLMOD code and methods
1212 :     for CsparseMatrix, TsparseMatrix, denseMatrix or matrix when
1213 :     possible.
1214 :    
1215 : bates 1368 2006-08-12 Douglas Bates <bates@R-project.org>
1216 :    
1217 :     * src/chm_common.[ch],Csparse.[ch],Tsparse.[ch],CHMfactor.c,dtTMatrix.c,
1218 :     dgTMatrix.c,dgCMatrix.c,dsCMatrix.c,dtTMatrix.c, R/dsTMatrix.R,
1219 :     Tsparse.R,Csparse.R,dgTMatrix.R,dsCMatrix.R,lsCMatrix.R:
1220 :     generalize conversions between TsparseMatrix, CsparseMatrix,
1221 :     denseMatrix and matrix. Preserve triangularity property and
1222 :     propagate Dimnames in the easy cases.
1223 :    
1224 : bates 1365 2006-08-10 Douglas Bates <bates@R-project.org>
1225 :    
1226 :     * src/lmer.c: adjust checks in glmer_init for S4SXP
1227 :     * tests/validObj.R: check of all(eq) should be all(eq@x) - worked
1228 :     before S4SXP but for the wrong reasons.
1229 :    
1230 : bates 1354 2006-08-08 Douglas Bates <bates@R-project.org>
1231 :    
1232 : bates 1360 * src/Csparse.c (Csparse_crossprod): tcrossprod result has stype = -1.
1233 :     Later modified to return the upper triangle only.
1234 :     * R/dgTMatrix.R: Remove vestigial crossprod and tcrossprod methods.
1235 : maechler 1389
1236 : bates 1352 2006-08-07 Douglas Bates <bates@R-project.org>
1237 :    
1238 :     * src/Csparse.c (Csparse_crossprod): Set stype on result to avoid
1239 :     R-level conversion to a sparse symmetric class.
1240 :     * R/Tsparse.R,R/Csparse.R (crossprod and tcrossprod methods):
1241 :     Remove conversion to sparse symmetric classes (now done in C code).
1242 :    
1243 : maechler 1349 2006-08-07 Martin Maechler <maechler@stat.math.ethz.ch>
1244 :    
1245 : maechler 1351 * R/dgCMatrix.R: disable old crossprod and tcrossprod methods
1246 :     * man/band.Rd: adapt the \dontshow{} unit test.
1247 :    
1248 :     2006-08-07 Martin Maechler <maechler@stat.math.ethz.ch>
1249 :    
1250 : maechler 1349 * DESCRIPTION (Version): 0.995-14 for CRAN
1251 :    
1252 :     * tests/other-pkgs.R: oops: library(Matrix) outside *if* !
1253 :    
1254 :     * R/sparseMatrix.R (Tsp2grNEL): fixed Tsparse -> graph coercion
1255 :     * tests/other-pkgs.R: more checks, sparseMatrix -> graph
1256 :    
1257 :     * R/Auxiliaries.R (as_Tsparse, as_Rsparse): new
1258 :     * R/Tsparse.R (tril, triu, band): methods
1259 : bates 1352 * R/dgRMatrix.R (tril, ...): ditto
1260 :     * man/band.Rd: ditto
1261 : maechler 1349
1262 :     2006-08-04 Martin Maechler <maechler@stat.math.ethz.ch>
1263 :    
1264 :     * R/Matrix.R (head, tail): directly use utils:::head.matrix
1265 :     to be up-to-date automatically.
1266 :    
1267 : maechler 1346 2006-08-03 Martin Maechler <maechler@stat.math.ethz.ch>
1268 :    
1269 :     * DESCRIPTION (Version): 0.995-13 to be released to CRAN
1270 :    
1271 :     * DESCRIPTION (Lazydata): no, instead of 'yes' because it fails for:
1272 :     * data/CAex.R, inst/external/CAex_slots.rda: replacing data/CAex.rda
1273 :     * data/KNex.R, inst/external/KNex_slots.rda: replacing data/KNex.rda
1274 :     such that the S4 objects are always created by the current version
1275 :     of R and 'Matrix' class definitions.
1276 :    
1277 : bates 1342 2006-08-01 Douglas Bates <bates@R-project.org>
1278 :    
1279 :     * R/lmer.R (LMEoptimize method), tests/lmer.R,
1280 : maechler 1346 inst/external/test3comp.rda: Added warnings for convergence on
1281 : bates 1342 boundary and test cases.
1282 :    
1283 :     * src/lmer.c (mer_postVar): Modified to return the variances that
1284 :     are marginal to the fixed effects, not conditional on them (which
1285 :     is what the bVar slot contents represent).
1286 :    
1287 : bates 1338 2006-07-31 Douglas Bates <bates@R-project.org>
1288 :    
1289 :     * NAMESPACE, src/lmer.c, R/lmer.R (hatTrace): Add the hatTrace
1290 :     function which calls the C function mer_hat_trace2.
1291 : maechler 1346
1292 : bates 1342 * man/ranef.Rd: Include description of "postVar" argument and
1293 :     producing a caterpillar plot.
1294 : bates 1338
1295 : maechler 1335 2006-07-31 Martin Maechler <maechler@stat.math.ethz.ch>
1296 :    
1297 :     * NAMESPACE: change "correlation" to "corMatrix"
1298 :     * R/AllClass.R: to avoid clash with S3 class in 'nlme'.
1299 : bates 1352 * R/dpoMatrix.R: ditto
1300 :     * R/lmer.R: ditto
1301 : maechler 1335
1302 : bates 1338 2006-07-28 Douglas Bates <bates@R-project.org>
1303 :    
1304 :     * src/lmer.c (internal_mer_RZXinv): Split the calculation of the
1305 :     RZXinv slot's contents into a separate internal function that can
1306 :     be used in mer_hat_trace.
1307 :    
1308 : maechler 1331 2006-07-22 Martin Maechler <maechler@stat.math.ethz.ch>
1309 :    
1310 :     * R/Matrix.R: Coercions "Matrix" -> (sparse|dense)Matrix
1311 :     via new smart
1312 :     * R/Auxiliaries.R (as_Csparse, as_dense, .M.shapse): new
1313 :     utility functions.
1314 :    
1315 :    
1316 : maechler 1330 2006-07-21 Martin Maechler <maechler@stat.math.ethz.ch>
1317 :    
1318 : maechler 1331 * R/Csparse.R (tril, triu, band): do return *triangular* classed
1319 :     matrices when appropriate; band() even symmetric ones.
1320 :     (replCmat): extend to potentially all "CsparseMatrix"
1321 :     * R/Tsparse.R (replTmat): extend to all "TsparseMatrix"; hence
1322 :     allow subassignment for special sparse matrices.
1323 :    
1324 :     * R/Auxiliaries.R (as_geClass): factor out the .M.kind() functionality
1325 :    
1326 : maechler 1330 * src/lmer.c (mer_MCMCsamp, glmer_MCMCsamp): new 'verbose'
1327 :     argument; in glmer_*(): print only if(verbose).
1328 :    
1329 :     speed-optimize a few places by moving REAL(.) out of loops.
1330 :    
1331 :     * src/lmer.h, src/init.h, R/lmer.R: related to above.
1332 :    
1333 : maechler 1329 2006-07-20 Martin Maechler <maechler@stat.math.ethz.ch>
1334 :    
1335 :     * R/Matrix.R("["): disable ("Matrix", i = "logical", j = "missing"),
1336 :     since that wrongly triggers also for M[ logi , ]
1337 :    
1338 :     * R/denseMatrix.R: "[" methods now also work e.g. when indexing
1339 :     a symmetric matrix that results in a non-symmetric one.
1340 :     * R/Auxiliaries.R (as_geClass): new function used in "[" above.
1341 :    
1342 :     * R/dMatrix.R: make round(M) work as round(M, 0)
1343 :    
1344 :     * R/dgTMatrix.R (image): coordinate system and axis now use
1345 :     1-based indices, not 0-based ones.
1346 :    
1347 :     * R/Tsparse.R (.ind.prep for "["): get rid of max(<empty>) warning.
1348 :     * tests/indexing.R: test it.
1349 :    
1350 :     * NAMESPACE: export isSymmetric(); has been a generic in "base" for a while;
1351 :     * man/isSymmetric-methods.Rd: and document it.
1352 :    
1353 :     * R/SparseM-conv.R: added coercion methods for some 'SparseM' matrices.
1354 :     * man/SparseM-conv.Rd: docu them
1355 :    
1356 :     * tests/other-pkgs.R: renamed from tests/graph.R and add example
1357 :     for 'SparseM' conversions
1358 :    
1359 :     2006-07-17 Douglas Bates <Douglas.Bates@R-project.org>
1360 :    
1361 :     * R/Matrix.R (head): added head() and tail() methods.
1362 :    
1363 :     2006-07-17 Martin Maechler <maechler@stat.math.ethz.ch>
1364 :    
1365 :     * DESCRIPTION (Version): 0.995-12 released to CRAN
1366 :    
1367 : maechler 1319 2006-07-15 Martin Maechler <maechler@stat.math.ethz.ch>
1368 :    
1369 :     * tests/simple.R: add check for correct dsT -> dgT coercion;
1370 :     add check for correct printing of symmetric sparse matrices.
1371 :    
1372 :     * R/Auxiliaries.R (non0ind): return *all* non-0 entry indices also
1373 :     for sparse symmetric matrices.
1374 :    
1375 :     * src/dsTMatrix.c (dsTMatrix_as_dgTMatrix): do not copy the
1376 :     diagonal twice.
1377 :    
1378 : bates 1316 2006-07-11 Douglas Bates <Douglas.Bates@R-project.org>
1379 :    
1380 :     * src/dsTMatrix.c (dsTMatrix_as_dgTMatrix): Fix a case of INTEGER
1381 : maechler 1319 being applied to the x slot (detected by Brian Ripley).
1382 : bates 1316
1383 : maechler 1315 2006-07-10 Martin Maechler <maechler@stat.math.ethz.ch>
1384 :    
1385 :     * src/dgCMatrix.c (dgCMatrix_validate): 'p' slot must have correct length.
1386 :    
1387 :     * R/Auxiliaries.R (isTriC): fix buglet (we were 1-based!)
1388 :    
1389 :     2006-07-08 Martin Maechler <maechler@stat.math.ethz.ch>
1390 :    
1391 :     * src/lgCMatrix.c (lgCMatrix_diag): new function
1392 :     * R/lgCMatrix.R (diag): for new method
1393 :    
1394 :     * R/AllClass.R (TsparseMatrix): do use Tsparse_validate
1395 :     ==> construction of illegal "*gTMatrix" via new() should
1396 :     now be much less easy:
1397 :     * tests/Class+Meth.R: assertError() for some illegal "dgT*"
1398 :    
1399 :     * R/Matrix.R (Matrix): Matrix(0, nrow,ncol) now "goes sparse"
1400 :     directly.
1401 :     * man/Matrix.Rd: documents it.
1402 :    
1403 : bates 1311 2006-07-06 Douglas Bates <bates@R-project.org>
1404 :    
1405 :     * src/pedigree.c (pedigree_inbreeding): Correction in
1406 :     initialization. This function is not currently being used and is
1407 :     not fully tested.
1408 :    
1409 : bates 1312 * NAMESPACE, R/{AllClass.R,lmer.R}, src/{init.c,lmer.c}:
1410 :     Introduced the glmer class. Added code for mcmcmsamp on glmer
1411 :     objects. Modified validity check on pedigree objects to account
1412 :     for nonparallel patterns of missingness of parents.
1413 : bates 1311
1414 : bates 1313 * man/{lmer-class.Rd,mcmcsamp.Rd}: Update documentation for glmer
1415 :     class.
1416 : maechler 1315
1417 :     2006-07-01 Martin Maechler <maechler@stat.math.ethz.ch>
1418 :    
1419 :     * R/pMatrix.R: coercion pMatrix -> Tsparse
1420 :    
1421 : bates 1300 2006-06-12 Douglas Bates <bates@R-project.org>
1422 :    
1423 : maechler 1319 * DESCRIPTION (Version): 0.995-11 released to CRAN
1424 :    
1425 : bates 1300 * R/lmer.R (mcmcsamp method): Corrected arrangments of names on
1426 :     the output from mcmcsamp.
1427 :    
1428 : bates 1298 2006-06-10 Douglas Bates <bates@R-project.org>
1429 :    
1430 : bates 1300 * R/lmer.R (simulestimate): added C code for calculating the trace
1431 :     of the hat matrix.
1432 : bates 1298
1433 : maechler 1295 2006-06-09 Martin Maechler <maechler@stat.math.ethz.ch>
1434 :    
1435 :     * R/diagMatrix.R (setAs): define coercion methods to sparse matrix
1436 :     classes.
1437 : maechler 1315 * R/sparseMatrix.R etc: multiplication of diagonal and sparse
1438 : maechler 1295
1439 : maechler 1290 2006-06-08 Martin Maechler <maechler@stat.math.ethz.ch>
1440 :    
1441 :     * R/dgTMatrix.R (colSums): etc. All four of
1442 :     colSums(), rowSums(), colMeans(), rowMeans() now should work for
1443 :     all "Matrices".
1444 :    
1445 : bates 1288 2006-06-01 Douglas Bates <bates@stat.wisc.edu>
1446 :    
1447 :     * R/lmer.R (panel.ci): Add a reference line at zero and a
1448 :     background grid to the qqmath plot of ranef.lmer.
1449 :    
1450 : bates 1287 2006-05-30 Douglas Bates <bates@stat.wisc.edu>
1451 : bates 1284
1452 : bates 1287 * R/lmer.R (expandSlash): Functions (non-exported) to allow nested
1453 :     grouping factors to be specified in the formula as (1|foo/bar).
1454 :    
1455 :     2006-05-27 Douglas Bates <bates@stat.wisc.edu>
1456 :    
1457 : bates 1284 * R/lmer.R (findbars and others): Change check of is.numeric to
1458 :     !is.language to resolve the bug reported by Jacob Wegelin.
1459 :    
1460 :     * src/pedigree.c (pedigree_inbreeding): Initial implementation of
1461 :     code to evaluate inbreeding coefficients without calculating T,
1462 :     based on code in Sargolzaei and Iwaisaki's paper.
1463 :    
1464 : bates 1283 2006-05-27 Douglas Bates <bates@stat.wisc.edu>
1465 :    
1466 :     * R/{lmer.R,AllGeneric.R}, src/{init.c,lmer.[ch]}: Added local
1467 :     generic and mer methods for isNested and denomDF. This denomDF was
1468 :     an attempt to emulate that in lme but I don't think that makes
1469 :     sense. Use the trace of the hat matrix instead.
1470 :    
1471 : maechler 1271 2006-05-17 Martin Maechler <maechler@stat.math.ethz.ch>
1472 :    
1473 :     * R/sparseMatrix.R: Matrix <-> graph methods: can no longer use
1474 :     the C code depending on a slot structure that's no longer valid.
1475 : bates 1352 * src/dgTMatrix.c: ditto (also: src/init.c src/dgTMatrix.h)
1476 : maechler 1271
1477 :    
1478 : bates 1268 2006-05-17 Douglas Bates <bates@stat.wisc.edu>
1479 :    
1480 :     * R/{AllGeneric.R,Csparse.R},man/band.Rd,NAMESPACE: changed name
1481 :     of lowerTriMatrix generic and methods to tril (also upper to triu)
1482 :     and added a general band extractor.
1483 :    
1484 : bates 1267 2006-05-16 Douglas Bates <bates@stat.wisc.edu>
1485 :    
1486 :     * R/pedigree.R (pedigree): Replace sire and dam values outside the
1487 :     allowable range with NAs. Added a corresponding check in the
1488 :     validity check for the pedigree class.
1489 :    
1490 :     * R/[CT]sparse.R ([t]crossprod): The result of single-argument
1491 :     crossprod methods now inherits from symmetricMatrix.
1492 :    
1493 : bates 1265 2006-05-15 Douglas Bates <bates@stat.wisc.edu>
1494 :    
1495 :     * R/AllGeneric.R (lowerTriMatrix): Added (but did not export)
1496 :     generics lowerTriMatrix and upperTriMatrix along with methods for
1497 :     the Csparse virtual class. Also added a C function Csparse_band
1498 :     that implements these methods by calling cholmod_band.
1499 :    
1500 : maechler 1264 2006-05-15 Martin Maechler <maechler@stat.math.ethz.ch>
1501 :    
1502 :     * R/Tsparse.R ("["): column or row subsetting; @Dimnames[k] got
1503 :     erased when it was NULL. This led to invalid subselections!
1504 :    
1505 : bates 1259 2006-04-25 Douglas Bates <bates@stat.wisc.edu>
1506 :    
1507 :     * R/dtCMatrix.R: avoid coercion of dtCMatrix object to dgCMatrix
1508 :     in method for "t" so as not to lose the unit diagonal property.
1509 :    
1510 : bates 1257 2006-04-19 Douglas Bates <bates@stat.wisc.edu>
1511 :    
1512 :     * R/lmer.R, R/AllGeneric.R, NAMESPACE: Remove the postVar generic
1513 :     and methods. This is now an option to the ranef method for the
1514 :     mer class.
1515 :    
1516 :     * src/cs_utils.c: Ensure that the nz component is -1 for a
1517 :     compressed column-oriented matrix. Minor formatting cleanup.
1518 :    
1519 :     * man/lmer-class.Rd: Document the qqmath method for ranef.lmer
1520 :     objects.
1521 :    
1522 : maechler 1253 2006-04-19 Martin Maechler <maechler@stat.math.ethz.ch>
1523 :    
1524 :     * R/Auxiliaries.R (diagU2N): new for the solve() methods in
1525 :     * R/dtCMatrix.R: where dgC -> dgT coercion now preserves diag = "U".
1526 :    
1527 : bates 1251 2006-04-15 Douglas Bates <bates@stat.wisc.edu>
1528 :    
1529 :     * src/cs.[ch],src/cs_utils.[ch] : Added Tim Davis' CSparse library
1530 :     in cs.[ch] and utilities to interface to that code in cs_utils.[ch].
1531 :    
1532 :     * R/dtCMatrix.R, src/dtCMatrix.[ch] : CSparse-based solve methods
1533 :     for the dtCMatrix class.
1534 : maechler 1253
1535 : bates 1247 2006-04-12 Douglas Bates <bates@stat.wisc.edu>
1536 :    
1537 :     * R/pedigree.R, R/AllClass.R, NAMESPACE: added a pedigree class
1538 :     and methods for it.
1539 :    
1540 : maechler 1245 2006-04-12 Martin Maechler <maechler@stat.math.ethz.ch>
1541 :    
1542 :     * R/dgCMatrix.R: add storage.mode(.) <- "double" for "matrix"
1543 :     arguments, such that M %*% 1:6 now works
1544 :     * Tests/matprod.R: test the above
1545 :    
1546 : bates 1244 2006-04-03 Douglas Bates <bates@stat.wisc.edu>
1547 : bates 1243
1548 :     * R/lmer.R (qqmath,ranef.lmer-method): added a qqmath method for
1549 :     the ranef.lmer class.
1550 :    
1551 :     * R/AllClass.R, NAMESPACE, R/lmer.R: Added a postVar generic and
1552 :     methods to extract the posterior variances from the bVar slot.
1553 :    
1554 : maechler 1238 2006-03-30 Martin Maechler <maechler@stat.math.ethz.ch>
1555 :    
1556 :     * R/dtCMatrix.R: allow coercion from dgC* to triangular (dtC*)
1557 :     * R/dsCMatrix.R: and symmetric (dsC*) 'Csparse' matrices.
1558 :    
1559 :     * R/Tsparse.R: Tsparse* -> Csparse* coercion now works and is tested in
1560 :     * tests/simple: (extended)
1561 :    
1562 :     * R/sparseMatrix.R (isTriangular): now using much improved
1563 :     * R/Auxiliaries.R (isTriC): new triangularity check for *CMatrix
1564 :    
1565 : bates 1236 2006-03-23 Douglas Bates <bates@stat.wisc.edu>
1566 :    
1567 :     * src/dsyMatrix.c (dsyMatrix_as_dspMatrix): Propagate DimNames
1568 :     (problem report from Franklin Parlamis). This should be done
1569 : maechler 1238 generally.
1570 : bates 1236
1571 : bates 1234 2006-03-21 Douglas Bates <bates@stat.wisc.edu>
1572 :    
1573 :     * R/AllClass.R,lmer.R: Change the name of the lmer.ranef class to
1574 :     ranef.lmer (like summary.lmer). Add the coef.lmer class and
1575 :     update the plot methods.
1576 :    
1577 : bates 1232 2006-03-20 Douglas Bates <bates@stat.wisc.edu>
1578 :    
1579 :     * R/lmer.R (resid and ranef methods): Added methods for the
1580 :     "residuals" and "resid" generic but only for linear mixed model
1581 :     fits. Changed the ranef method to return a list of data frames so
1582 :     that the plot methods now work.
1583 :    
1584 : bates 1230 2006-03-16 Douglas Bates <bates@bates2>
1585 :    
1586 :     * src/dpoMatrix.c (dpoMatrix_chol): Require n > 0 in call to
1587 :     dpotrf - otherwise the BLAS on Mac OS X complains and quits.
1588 :    
1589 :     * DESCRIPTION (Date): New release
1590 :    
1591 : maechler 1228 2006-03-15 Martin Maechler <maechler@stat.math.ethz.ch>
1592 :    
1593 :     * DESCRIPTION (Version): 0.995-6 -- to be released to CRAN
1594 :    
1595 :     * data/KNex.rda: replacing 'mm' and 'y' by KNex <- list(mm=mm, y=y)
1596 :     * man/KNex.Rd: and other help files
1597 :     * tests/*.R: several ones needed adaption
1598 : bates 1352 * inst/doc/Comparisons.Rnw: ditto
1599 : maechler 1228
1600 : maechler 1226 2006-03-11 Martin Maechler <maechler@stat.math.ethz.ch>
1601 :    
1602 :     * R/dgCMatrix.R (replCmat): "[<-" methods for dgCMatrix
1603 :    
1604 :     * tests/indexing.R: tests for new [<- methods for sparse matrices.
1605 :    
1606 :     2006-03-10 Martin Maechler <maechler@stat.math.ethz.ch>
1607 :    
1608 :     * R/dgTMatrix.R (replTmat): "[<-" methods for dgTMatrix
1609 :    
1610 :     * R/Tsparse.R (.ind.prep): fix out-of-range indexing
1611 :    
1612 :     2006-03-08 Martin Maechler <maechler@stat.math.ethz.ch>
1613 :    
1614 :     * R/dMatrix.R: enable things like M [ M < 10 ]
1615 :     * R/dgeMatrix.R: implement it
1616 :    
1617 : maechler 1222 2006-03-06 Martin Maechler <maechler@stat.math.ethz.ch>
1618 :    
1619 :     * R/AllClass.R: define "summary.mer" and "*.lmer"
1620 :     * R/lmer.R (summary): summary(<mer>) computes & returns the above;
1621 :     * R/lmer.R (show): now works with summary()
1622 :    
1623 :     2006-03-04 Martin Maechler <maechler@stat.math.ethz.ch>
1624 :    
1625 :     * R/dgCMatrix.R: finally direct "Arith" dgC o dgC
1626 :     * R/Auxiliaries.R (WhichintersectInd): and other utilities to
1627 :     support the above
1628 :    
1629 : bates 1213 2006-02-07 Douglas Bates <bates@stat.wisc.edu>
1630 :    
1631 :     * R/lmer.R (lmer): fix initial values of offset and weights for glm.fit.
1632 :     Use glmFit$prior.weights for weights in a glmm.
1633 :     Allow an option usePQL = FALSE to skip the PQL steps for the
1634 :     Laplace method (and, in time, the AGQ method).
1635 :    
1636 :     * src/lmer.c (mer_factor): Move downdating and factoring of XtX
1637 :     into a separate function internal_mer_Xfactor to be able to call
1638 :     it from internal_bhat.
1639 :    
1640 : maechler 1200 2006-01-23 Martin Maechler <maechler@stat.math.ethz.ch>
1641 :    
1642 :     * tests/Class+Meth.R (tstMatrixClass): function for much better
1643 :     testing; now again of all actual classes.
1644 :    
1645 :     * src/Mutils.c (MAKE_TRIANGULAR_BODY, MAKE_SYMMETRIC_BODY):
1646 :     use macros and define make_d_matrix_* and make_i_matrix_*
1647 :     where _i_ is for the ldense routines:
1648 :    
1649 :     * src/ldense.c (ltrMatrix_as_lgeMatrix): provide functions
1650 :     * src/ldense.c (lsyMatrix_as_lgeMatrix):
1651 :    
1652 :     * R/ldenseMatrix.R: use the above in setAs(*,"lgeMatrix")
1653 :    
1654 :    
1655 : maechler 1174 2006-01-16 Martin Maechler <maechler@stat.math.ethz.ch>
1656 :    
1657 :     * R/Matrix.R (Matrix): has become much "smarter" now auto-producing
1658 :     many different kinds of matrices.
1659 :     * R/*.R: quite a few new methods were needed for R CMD check with
1660 :     new Matrix(). Very good for users playing around.
1661 :    
1662 :    
1663 : maechler 1165 2006-01-15 Martin Maechler <maechler@stat.math.ethz.ch>
1664 :    
1665 :     * src/dgeMatrix.c (dMatrix_validate): new
1666 :     * src/Mutils.c (dense_nonpacked_validate): new
1667 :    
1668 :     * src/dtrMatrix.c (dtrMatrix_validate): improved/fixed
1669 :    
1670 :    
1671 :     2006-01-14 Douglas Bates <bates@stat.wisc.edu>
1672 :    
1673 :     * R/AllClass.R (compMatrix), (generalMatrix): new virtual classes
1674 :    
1675 : bates 1123 2006-01-07 Douglas Bates <bates@stat.wisc.edu>
1676 : bates 1119
1677 : maechler 1127 * DESCRIPTION (Version): 0.99-6 released to CRAN
1678 :    
1679 : bates 1119 * src/dgBCMatrix.c (cscb_trcbsm): Fix due to Peter Dalgaard for
1680 :     segfault in cases with multiple non-nested grouping factors.
1681 :    
1682 : maechler 1109 2006-01-03 Martin Maechler <maechler@stat.math.ethz.ch>
1683 :    
1684 :     * DESCRIPTION (Version): 0.99-4 to be released to CRAN
1685 :     (Depends): also on 'utils'
1686 :    
1687 :     * R/AllClass.R (diagonalMatrix): new class with "ddi*" and "ldi*"
1688 :     * R/diagMatrix.R (Diagonal): constructor and methods for
1689 :     diagonal matrices
1690 :    
1691 :     * R/ltTMatrix.R: new "minimal methods"
1692 :    
1693 : maechler 1091 2005-12-12 Martin Maechler <maechler@stat.math.ethz.ch>
1694 :    
1695 :     * R/AllGeneric.R (tcrossprod): 2-argument version; here, and for
1696 :     all methods (and help files).
1697 :    
1698 : maechler 1084 2005-12-09 Martin Maechler <maechler@stat.math.ethz.ch>
1699 :    
1700 :     * R/Auxiliaries.R (dimNamesCheck): fixed thinko -> bug
1701 :     for case (dimn. op no_dimn.)
1702 :    
1703 :     2005-11-14 Douglas Bates <bates@stat.wisc.edu>
1704 :    
1705 : maechler 1174 * DESCRIPTION (Version): 0.99-2 released to CRAN
1706 : maechler 1084
1707 : bates 988 2005-10-21 Douglas Bates <bates@stat.wisc.edu>
1708 :    
1709 :     * R/lmer.R (simulate method): Fixed a drop=FALSE problem reported
1710 :     by Julian Faraway.
1711 :    
1712 : maechler 976 2005-10-06 Martin Maechler <maechler@stat.math.ethz.ch>
1713 :    
1714 :     * R/Auxiliaries.R (try_as): new utility
1715 :     * R/sparseMatrix.R: use try_as() in coercion to original class
1716 :    
1717 : maechler 956 2005-09-30 Martin Maechler <maechler@stat.math.ethz.ch>
1718 :    
1719 :     * src/dgCMatrix.c (double_to_csc): and dgeMatrix_to_csc()
1720 :    
1721 :     2005-09-29 Martin Maechler <maechler@stat.math.ethz.ch>
1722 :    
1723 :     * R/Auxiliaries.R (dimNamesCheck): added
1724 :    
1725 :     * R/Matrix.R (as.array), (as.vector): new
1726 :    
1727 : maechler 954 2005-09-28 Martin Maechler <maechler@stat.math.ethz.ch>
1728 :    
1729 :     * R/Matrix.R (Matrix): get logical argument 'sparse' with a smart
1730 : maechler 956 default.
1731 :     * R/AllClass.R: move 'factors' slot toplevel "Matrix";
1732 :     "pMatrix" now contains "sparseMatrix"
1733 : maechler 954
1734 : maechler 948 2005-09-26 Martin Maechler <maechler@stat.math.ethz.ch>
1735 :    
1736 :     * tests/Class+Meth.R: new tests; t(t(m)) == m
1737 :    
1738 :     * src/dtCMatrix.c (tsc_transpose): add forgotten "diag" slot
1739 :    
1740 :     * src/dsTMatrix.c (dsTMatrix_as_dsCMatrix): bad typo (segfault!)
1741 :     * src/dtTMatrix.c (dtTMatrix_as_dtCMatrix): new
1742 :    
1743 :     * R/dspMatrix.R: typo in "t" method
1744 :    
1745 : maechler 925 2005-09-18 Douglas Bates <bates@wisc.edu>
1746 :    
1747 :     * R/AllClass.R (TsparseMatrix), CsparseM* and RsparseM*
1748 :     * R/Tsparse.R: instead of R/gTMatrix.R
1749 :     * R/Csparse.R: new
1750 :     * src/Tsparse.c (Tsparse_to_Csparse): new; -> cholmod_()
1751 :     * src/Tsparse.c: new; many trivial methods calling cholmod_()
1752 :     * src/Csparse.c (Csparse_to_Tsparse), transpose, (mat|cross)prod:
1753 :     via cholmod
1754 :    
1755 :     2005-09-16 Martin Maechler <maechler@stat.math.ethz.ch>
1756 :    
1757 :     * R/Auxiliaries.R (non0ind): new function using new C code
1758 :     * src/dgCMatrix.c (compressed_non_0_ij): new utility
1759 :    
1760 : bates 917 2005-09-15 Douglas Bates <bates@localhost.localdomain>
1761 :    
1762 :     * src/chm_common.h: header file required by all C sources that
1763 : maechler 1174 call CHOLMOD functions. It defines a cholmod_common structure
1764 : bates 917 called 'c' whose address is passed as the last argument to
1765 :     (virtually) every CHOLMOD function.
1766 :    
1767 :     * src/Pattern.c: Simple example of the use of CHOLMOD.
1768 :    
1769 :     * src/init.c: initialize and finalize the cholmod_common structure.
1770 :    
1771 :     * src/Makefile: Added source packages CHOLMOD UMFPACK AMD COLAMD
1772 :     LDL and CCOLAMD from the U. of Florida sparse matrix library.
1773 :    
1774 : maechler 908 2005-09-08 Martin Maechler <maechler@stat.math.ethz.ch>
1775 :    
1776 :     * inst/test-tools.R: new file collecting the utility functions used
1777 :     in ./tests/*.R
1778 :    
1779 :     * R/ddenseMatrix.R (cbind2): new methods for "numeric" and "matrix"
1780 :     * R/Matrix.R (cbind2): methods for NULL and missing
1781 :    
1782 : maechler 886 2005-08-31 Martin Maechler <maechler@stat.math.ethz.ch>
1783 :    
1784 :     * R/AllClass.R: new "index" class for "[" and "[<-":
1785 :     First cut at "symmetricMatrix" and "triangularMatrix"
1786 :     * R/gTMatrix.R (.ind.prep): new function;
1787 : maechler 1174 Logical and character indexing now work too.
1788 : maechler 886 * R/Matrix.R: cheap "[<-" methods for denseMatrix now work
1789 :     * tests/indexing.R: new, including *.Rout.save
1790 :     * tests/dgTMatrix.R: new
1791 :    
1792 : bates 876 2005-08-29 Douglas Bates <bates@wisc.edu>
1793 :    
1794 :     * src/dgTMatrix.c (graphNEL_as_dgTMatrix): Corrected the position
1795 :     indicator pos not being updated. Also enforced upper triangular
1796 :     for symmetric case. Need to coerce edges component of elements of
1797 :     edge list - grr! (Why don't they define their classes cleanly?)
1798 :    
1799 : maechler 871 2005-08-26 Martin Maechler <maechler@stat.math.ethz.ch>
1800 :    
1801 :     * R/Matrix.R: added first "[<-" methods; not yet functional
1802 : bates 1352 * R/denseMatrix.R: ditto
1803 : maechler 871 * man/Subassign-methods.Rd: new help file for these
1804 :    
1805 :     2005-08-25 Martin Maechler <maechler@stat.math.ethz.ch>
1806 :    
1807 :     * DESCRIPTION (Version): 0.98-6
1808 :    
1809 :     * R/denseMatrix.R: new file for "[" fallback methods for all dense
1810 :     matrices.
1811 :    
1812 : maechler 868 2005-08-19 Martin Maechler <maechler@stat.math.ethz.ch>
1813 :    
1814 :     * src/lgCMatrix.c (lcsc_to_matrix): new; need for
1815 :     as( <logical>, "matrix")
1816 :    
1817 :     * R/pMatrix.R: coercion to "lgTMatrix"
1818 :    
1819 :     * R/gTMatrix.R: new virtual class to define "[" methods for.
1820 :     * man/gTMatrix-class.Rd:
1821 :     * General slight re-organization of where "[" methods are defined.
1822 :     more to come.
1823 :    
1824 : maechler 871 2005-08-18 Douglas Bates <bates@wisc.edu>
1825 : maechler 868
1826 : maechler 1174 * DESCRIPTION (Version): 0.98-5 released to CRAN
1827 : maechler 871
1828 :     * src/dgTMatrix.c (graphNEL_as_dgTMatrix): add first graphNEL methods
1829 :     * .....
1830 :    
1831 : bates 863 2005-08-18 Douglas Bates <bates@localhost.localdomain>
1832 :    
1833 :     * R/lmer.R: Corrected naming scheme in mcmcsamp to work with lmer
1834 :     or glmer objects.
1835 :    
1836 : maechler 860 2005-08-17 Martin Maechler <maechler@stat.math.ethz.ch>
1837 :    
1838 :     * DESCRIPTION (Version): 0.98-4 : upload to CRAN
1839 :    
1840 :     2005-08-16 Douglas Bates <bates@localhost.localdomain>
1841 :    
1842 :     * R/HBMM.R: finish re-writing R-only code.
1843 :    
1844 : bates 854 2005-08-15 Douglas Bates <bates@localhost.localdomain>
1845 :    
1846 :     * man/externalFormats.Rd: move documentation for writeHB and
1847 :     writeMM here.
1848 :    
1849 :     * src/mmio.c: replace inclusion of <malloc.h> by <stdlib.h>
1850 :     (suggested by Paul Roecker).
1851 :    
1852 :     * tests/validObj.R (assertError): Comment out test that is failing
1853 :     after recent changes in r-devel.
1854 :    
1855 : maechler 860
1856 : maechler 848 2005-08-11 Martin Maechler <maechler@stat.math.ethz.ch>
1857 :    
1858 :     * R/AllClass.R: intermediate virtual class "denseMatrix"
1859 :     * man/denseMatrix-class.Rd
1860 :     * NAMESPACE: export it, and also export
1861 :     * man/unused-classes.Rd: "iMatrix", "zMatrix" and "ldenseMatrix"
1862 :    
1863 : bates 846 2005-08-10 Douglas Bates <bates@wisc.edu>
1864 :    
1865 : maechler 848 * DESCRIPTION (Version): 0.98-3 to CRAN
1866 :    
1867 : bates 846 * src/dtrMatrix.c (dtrMatrix_validate): fixed up validation and
1868 :     matrix_solve code (which was really, really wrong).
1869 :    
1870 : bates 835 2005-08-07 Douglas Bates <bates@wisc.edu>
1871 : maechler 834
1872 :     * DESCRIPTION (Version): 0.98-2
1873 :    
1874 :     * R/HBMM.R (readHB), (readMM): read Matrix Market formats
1875 :    
1876 :     * R/lmer.R (abbrvNms): new
1877 :     * R/lmer.R (mcmcsamp): allow transformed parameters
1878 : bates 835 * src/HBMM.c (Matrix_writeMatrixMarket): Added read/write routines
1879 :     for the Harwell-Boeing and the MatrixMarket formats.
1880 : maechler 834
1881 :     2005-08-04 Martin Maechler <maechler@stat.math.ethz.ch>
1882 :    
1883 :     * man/dtrMatrix-class.Rd: add examples
1884 : bates 835 * man/dtpMatrix-class.Rd: ditto; plus note about PROBLEM
1885 : maechler 834
1886 :     * TODO: note the dtpMatrix (docu) bug
1887 :    
1888 :     * R/zzz.R (.onLoad): assignInNamespace("as.matrix", *, "base")
1889 :     in order to ensure that new as.matrix() is used by old functions,
1890 :     e.g., svd(), qr(), eigen(), dist(),..;
1891 :     apply(), also matplot() or pairs().
1892 :    
1893 :    
1894 :     2005-08-03 Martin Maechler <maechler@stat.math.ethz.ch>
1895 :    
1896 :     * R/lmer.R: add 'fixme' comments and move the linear vs glm check;
1897 :     add comments about 'control' / lmerControl() arguments
1898 :    
1899 : bates 835 2005-07-27 Douglas Bates <bates@wisc.edu>
1900 : bates 820
1901 : bates 835 * man/sleepstudy.Rd: Added the sleep data set.
1902 : maechler 1174 * DESCRIPTION (Version): 0.98-1 released to CRAN
1903 : bates 820
1904 : bates 835 2005-07-12 Douglas Bates <bates@wisc.edu>
1905 : maechler 834 * man/sleepstudy.Rd: Added the sleep data set.
1906 :    
1907 : bates 809 * R/lmer.R (glmmMCMC): Added PACKAGE = "Matrix" in a couple of
1908 :     .Call calls that were producing spurious output.
1909 :    
1910 : bates 835 2005-07-05 Douglas Bates <bates@wisc.edu>
1911 : bates 801
1912 :     * R/lmer.R (lmer): stored updated variance component estimates in
1913 :     mer object for the generalized model. (Bug reported by Renaud
1914 :     Lancelot).
1915 :    
1916 : bates 835 2005-07-03 Douglas Bates <bates@wisc.edu>
1917 : bates 794
1918 :     * src/lmer.c (glmer_devAGQ): Added AGQ for single grouping factor,
1919 :     unidimensional case.
1920 :    
1921 : bates 835 2005-06-08 Douglas Bates <bates@wisc.edu>
1922 : maechler 791
1923 :     * DESCRIPTION (Version): 0.96-1
1924 :    
1925 : maechler 1174 * moved lmer-class' R and C code moved from lme4 to here
1926 : maechler 791
1927 : bates 835 2005-06-04 Douglas Bates <bates@wisc.edu>
1928 : bates 763
1929 :     * R/dgCMatrix.R: Call to csc_matrix_mm used undefined arguments
1930 :     (reported by Guissepe Ragusa <gragusa@ucsd.edu>)
1931 :    
1932 : bates 835 2005-06-02 Douglas Bates <bates@wisc.edu>
1933 : bates 763
1934 :     * src/Makefile.win: Forgot to update this when Makefile changed.
1935 :    
1936 : bates 835 2005-05-11 Douglas Bates <bates@wisc.edu>
1937 : bates 726
1938 :     * src/dgCMatrix.c (csc_transpose): Simplified function fixing a
1939 :     bug reported by Kurt Hornik and Michael Hahsler.
1940 :    
1941 : bates 835 2005-05-10 Douglas Bates <bates@wisc.edu>
1942 : bates 725
1943 :     * src/lgCMatrix.c (Matrix_lgClgCmm): Implementation of methods for
1944 :     logical sparse matrices. These will also be used in the symbolic
1945 :     analysis for lmer objects.
1946 :    
1947 :     * src/dsCMatrix.c (dsCMatrix_matrix_solve): Copied the dimensions
1948 :     of b to the result. Fixes bug reported by Jean.Coursol@math.u-psud.fr
1949 : maechler 791
1950 : bates 835 2005-05-06 Douglas Bates <bates@wisc.edu>
1951 : bates 714
1952 :     * src/dgeMatrix.c (dgeMatrix_colsums): Added an implementation of
1953 :     colMeans, colSums, rowMeans and rowSums.
1954 :    
1955 : bates 835 2005-04-18 Douglas Bates <bates@wisc.edu>
1956 : bates 692
1957 :     * src/lgCMatrix.[ch]: code for _validate method and stub for
1958 :     multiplication operation.
1959 :    
1960 :     * src/dgeMatrix.c (dgeMatrix_matrix_solve): Passing wrong argument
1961 :     to dgetrs.
1962 :    
1963 :     * src/init.c: Fix cut-and-paste error in definition of
1964 :     dgeMatrix_matrix_solve
1965 :    
1966 :     * src/{many files}: Tighten code by using ALLOC_SLOT.
1967 :    
1968 : bates 835 2005-04-15 Douglas Bates <bates@wisc.edu>
1969 : bates 692
1970 :     * R/AllClass.R: Add lgTMatrix and lgCMatrix classes
1971 :    
1972 :     * DESCRIPTION: Eliminate import of stats.
1973 :    
1974 : maechler 791
1975 : bates 835 2005-04-06 Douglas Bates <bates@wisc.edu>
1976 : bates 692
1977 :     * R/AllClass.R : add logical sparse matrix classes
1978 :    
1979 : maechler 687 2005-04-01 Martin Maechler <maechler@stat.math.ethz.ch>
1980 :    
1981 :     * R/dgTMatrix.R: add "[" method for triplet matrices
1982 :     * R/sparseMatrix.R: and other sparse ones; --> add show() for sparse
1983 :    
1984 : bates 835 2005-03-31 Douglas Bates <bates@wisc.edu>
1985 : maechler 687
1986 :     * DESCRIPTION (Version): release 0.95-5 to CRAN
1987 :    
1988 :     * R/dMatrix.R: add %*%, crossprod and solve "fallback" methods
1989 :     * R/sparseMatrix.R: %*%, crossprod()
1990 :     * R/dgeMatrix.R: more "fallback" methods for numeric/dense matrices
1991 :     * man/*.Rd: move method definitions to 'Matrix' and 'dMatrix'
1992 :     * src/lmer.c (lmer_fitted): fix thinko
1993 :    
1994 : maechler 676 2005-03-26 Martin Maechler <maechler@stat.math.ethz.ch>
1995 :    
1996 :     * R/AllClass.R: add two virtual sparse classes ``on top''
1997 :    
1998 :     2005-03-24 Martin Maechler <maechler@stat.math.ethz.ch>
1999 :    
2000 :     * R/AllClass.R (setClass): use "VIRTUAL" for the virtual classes;
2001 :     correspondingly fix examples and tests/ since new()
2002 :     doesn't work for virtual classes.
2003 :    
2004 : maechler 658 2005-03-17 Martin Maechler <maechler@stat.math.ethz.ch>
2005 :    
2006 :     * R/Matrix.R (as.matrix): method and one for unname()
2007 :     * tests/dpoMatrix.R: tests should now be less platform dependent;
2008 :     also run for R 2.1.0; using as.matrix()
2009 :    
2010 : bates 835 2005-03-15 Douglas Bates <bates@wisc.edu>
2011 : maechler 658
2012 :     * R/pMatrix.R: "pMatrix" class added
2013 :     * ....
2014 :    
2015 : bates 835 2005-03-14 Douglas Bates <bates@wisc.edu>
2016 : bates 645
2017 :     * R/dtpMatrix.R: Add unpack method and an example.
2018 :    
2019 :     * src/dsyMatrix.c (dsyMatrix_trf): Add BunchKaufman factorization
2020 :     of general symmetric matrices and associated S4 methods.
2021 :    
2022 : maechler 658 2005-03-10 Martin Maechler <maechler@stat.math.ethz.ch>
2023 :     +
2024 :     2005-03-05 Martin Maechler <maechler@stat.math.ethz.ch>
2025 :    
2026 :     * R/dgeMatrix.R (setAs): and many other files: more coercion,
2027 :     crossprod() and "%*%" methods added; tests, too.
2028 :     * tests/matprod.R: new, for testing these
2029 :    
2030 : bates 835 2005-03-03 Douglas Bates <bates@wisc.edu>
2031 : bates 599
2032 :     * src/lmer.c (lmer_fitted): Added.
2033 :    
2034 : bates 835 2005-03-02 Douglas Bates <bates@wisc.edu>
2035 : bates 596
2036 :     * R/dsTMatrix.R: Conversion from dsTMatrix to dsCMatrix
2037 :    
2038 : bates 835 2005-02-28 Douglas Bates <bates@wisc.edu>
2039 : bates 582
2040 :     * src/*.c,po/,inst/po: Internationalization and localization of
2041 :     the package.
2042 :    
2043 :     * src/ldl.[ch]: Removed these as their contents are referenced in the
2044 :     R_ldl.c file.
2045 :    
2046 :     * src/flame.[ch]: Removed these source files.
2047 : maechler 658
2048 : bates 582 * src/dtrMatrix.c (make_array_triangular): Move to Mutils
2049 :    
2050 :     * src/LU.[ch],src/init.c: absorb in factorizations
2051 :    
2052 :     * src/Mutils.h: prepare for internationalization
2053 :    
2054 :     * src/cblas.h: move the enum definitions to Mutils.h and remove
2055 :     this file
2056 :    
2057 : maechler 578 2005-02-26 Martin Maechler <maechler@stat.math.ethz.ch>
2058 :    
2059 : maechler 579 * R/dgeMatrix.R: provide "dimnames" and "dimnames<-" methods
2060 :    
2061 :     * R/dtrMatrix.R: fix t() method
2062 :    
2063 : maechler 578 * R/dgeMatrix.R: define group methods "Arith", "Math", "Math2"
2064 : maechler 658 * NAMESPACE: export them (and import generics from "methods")
2065 : maechler 578 * tests/group-methods.R : and test them.
2066 :    
2067 :     * src/dtrMatrix.c (dtrMatrix_as_dgeMatrix): prevent seg.fault in
2068 :     border case
2069 :    
2070 :     2005-02-24 Douglas Bates <bates@stat.wisc.edu>
2071 :    
2072 : maechler 658 * DESCRIPTION (Version): 0.95-2 released to CRAN
2073 : maechler 578
2074 :     * src/dgBCMatrix.c:
2075 :     * src/lmer.c: many changes
2076 :     * ...
2077 :    
2078 : maechler 512 2005-02-04 Martin Maechler <maechler@stat.math.ethz.ch>
2079 :    
2080 :     * R/Matrix.R: add more sophisticated show() method.
2081 :    
2082 : maechler 578 2005-02-02 Douglas Bates <bates@stat.wisc.edu>
2083 :    
2084 :     * */* : almost complete reorganization of classes.
2085 :    
2086 : bates 835 2005-01-26 Douglas Bates <bates@wisc.edu>
2087 : bates 460
2088 :     * R/AllGeneric.R: Added matrix exponential generic expm and a method
2089 :     for the geMatrix class.
2090 :    
2091 : bates 835 2005-01-24 Douglas Bates <bates@wisc.edu>
2092 : bates 460
2093 :     * src/Makefile (clean): Remove *.a and *.so
2094 :    
2095 :     * man/cscBlocked-class.Rd: Remove reference to the lmer-class.
2096 :    
2097 : bates 835 2005-01-23 Douglas Bates <bates@wisc.edu>
2098 : bates 460
2099 : maechler 658 * src/lmer.c (Lind): Definition of Lind was backwards. This only
2100 : bates 460 had an effect in cases with more than 2 grouping factors.
2101 :    
2102 : bates 835 2005-01-03 Douglas Bates <bates@wisc.edu>
2103 : bates 415
2104 :     * src/lmeRep.c (lmer_variances): change from lmeRep to lmer
2105 :    
2106 : bates 835 2004-12-23 Douglas Bates <bates@wisc.edu>
2107 : bates 410
2108 :     * src/init.c (R_init_Matrix): Reorder calls to R_registerRoutines
2109 :     and R_useDynamicSymbols (suggested by B.D.Ripley).
2110 :    
2111 : bates 835 2004-12-14 Douglas Bates <bates@wisc.edu>
2112 : bates 392
2113 :     * R/sscMatrix.R: Add determinant methods
2114 :    
2115 :     * src/triplet.[ch],src/init.c (triplet_to_matrix): Add a coercion
2116 :     for tripletMatrix to matrix.
2117 :    
2118 : bates 835 2004-12-13 Douglas Bates <bates@wisc.edu>
2119 : bates 388
2120 : bates 392 * R/AllClass.R (.onLoad): Eliminate the bbCrosstab class, which is
2121 :     no longer used.
2122 :    
2123 : bates 388 * src/R_ldl.c: Created an R-specific version of the ldl.[ch] files
2124 :     with dynamic allocation of scratch arrays.
2125 :    
2126 :     * src/ssclme.c (ssclme_copy_ctab): Fixed bug in creation of ZtZ
2127 :     for multivariate random effects with multiple grouping factors.
2128 :     Fixes part but not all of #15.
2129 :    
2130 : bates 835 2004-12-03 Douglas Bates <bates@wisc.edu>
2131 : bates 375
2132 :     * src/lmeRep.c (lmeRep_factor): order of operations for multiple
2133 :     scalar grouping factors corrected.
2134 :    
2135 : bates 835 2004-11-29 Douglas Bates <bates@wisc.edu>
2136 : bates 375
2137 :     * src/bCrosstab.c: remove diag_update which is no longer used
2138 :    
2139 : bates 835 2004-11-16 Douglas Bates <bates@wisc.edu>
2140 : bates 350
2141 :     * src/Metis_utils.c: Move metis.h include to C sources so that the
2142 :     .h file can be included.
2143 :    
2144 : bates 835 2004-11-12 Douglas Bates <bates@wisc.edu>
2145 : bates 342
2146 : bates 350 * src/LU.c,geMatrix.c,trMatrix.c, etc.:
2147 : bates 342 Complete allocation of slots in NEW_OBJECT.
2148 :    
2149 :     * src/Mutils.h: Moved list of symbols to an include file
2150 :    
2151 : bates 835 2004-11-11 Douglas Bates <bates@wisc.edu>
2152 : bates 342
2153 :     * src/geMutils.c (Matrix_init): remove unused function
2154 :    
2155 : bates 835 2004-11-10 Douglas Bates <bates@wisc.edu>
2156 : bates 342
2157 :     * src/cscMatrix.c (csc_to_imagemat): removed unused function
2158 :    
2159 : bates 835 2004-11-05 Douglas Bates <bates@wisc.edu>
2160 : bates 327
2161 :     * src/Makefile.win (SOURCES_C): Keep consistent with Makefile
2162 :    
2163 : bates 835 2004-10-27 Douglas Bates <bates@wisc.edu>
2164 : bates 303
2165 :     * R/pdmatrix.R: remove PACKAGE="Matrix" in .Call calls
2166 :    
2167 : bates 835 2004-10-04 Douglas Bates <bates@wisc.edu>
2168 : bates 296
2169 :     * src/init.c: Created R_init_Matrix and added registration of C
2170 :     routines.
2171 :    
2172 : bates 835 2004-10-02 Douglas Bates <bates@wisc.edu>
2173 : bates 283
2174 :     * R/tripletMatrix.R: Force a require(lattice) for the image methods.
2175 :    
2176 : bates 835 2004-06-15 Douglas Bates <bates@wisc.edu>
2177 : bates 229
2178 :     * man/trMatrix-class.Rd: Escape the % chars in .Rd files.
2179 :    
2180 : bates 111 2004-04-20 Douglas Bates <bates@stat.wisc.edu>
2181 :    
2182 :     * src/Makefile.win ($(SHLIB)): Modifications per Uwe Ligges.
2183 :    
2184 : bates 109 2004-04-19 Douglas Bates <bates@stat.wisc.edu>
2185 :    
2186 :     * src/ssclme.c (ssclme_update_mm): fix logic error in
2187 :     ssclme_update_mm
2188 :    
2189 : bates 105 2004-04-18 Douglas Bates <bates@stat.wisc.edu>
2190 :    
2191 :     * src/ssclme.c (ssclme_coef, ssclme_coefGets): Create consistency
2192 :     in the order of unconstrained and constrained parameters.
2193 :     (ssclme_gradient): Added the gradients (not yet correct for
2194 :     multidimensional, unconstrained case).
2195 :    
2196 : bates 78 2004-04-14 Douglas Bates <bates@stat.wisc.edu>
2197 :    
2198 :     * src/ssclme.c (ssclme_EMsteps): Fix logic in REML update
2199 :    
2200 :     * src/Makefile.win: Remove unneeded ranlib call
2201 :    
2202 : bates 71 2004-04-12 Douglas Bates <bates@stat.wisc.edu>
2203 :    
2204 :     * DESCRIPTION (Version): New release
2205 :    
2206 :     * src/Makefile.win: Update Makefile.win to umfpack removal.
2207 :    
2208 : bates 49 2004-04-05 Douglas Bates <bates@bates2_home>
2209 :    
2210 :     * src/triplet_to_col.c: Create triplet_to_col as a native
2211 : maechler 658 function, not the version from umfpack. There were problems with
2212 : bates 49 the configuration of UMFPACK for 64-bit processors and there was
2213 :     only one umfpack routine being used so I moved it here.
2214 :    
2215 : bates 45 2004-04-04 Douglas Bates <bates@bates2_home>
2216 :    
2217 :     * src/ssclme.c (ssclme_variances): New function.
2218 :    
2219 : bates 28 2004-03-28 Douglas Bates <bates@bates2_home>
2220 :    
2221 :     * src/ssclme.c (ssclme_fitted): Added function.
2222 :    
2223 : bates 22 2004-03-27 Douglas Bates <bates@bates2_home>
2224 :    
2225 :     * src/ssclme.c (ssclme_transfer_dimnames): Add new function to
2226 :     store the dimnames in the XtX and bVar slots
2227 :     (ssclme_update_mm): Change the dimensions of the bVar slot
2228 :     components and the returned value from ssclme_ranef.
2229 :    
2230 : bates 10 2004-03-18 Douglas Bates <bates@stat.wisc.edu>
2231 :    
2232 :     * R/{pdMat.R,pdIdent.R,pdLogChol.R,pdMatrixLog.R,pdNatural.R},
2233 :     src/{pdMat.c,pdIdent.c,pdLogChol.c,pdNatural.c},
2234 :     tests/{pdCompSymm.R,pdDiag.R,pdIdent.R,pdLogChol.R,pdNatural.R},
2235 :     man/{pdMat-class.Rd,pdmatrix-class.Rd,corrmatrix-class.Rd,
2236 :     pdDiag-class.Rd,pdIdent-class.Rd,pdNatural-class.Rd,
2237 :     pdLogChol-class.Rd,coefGets.Rd,pdCompSymm-class.Rd,
2238 :     pdfactor-class.Rd,pdFactor.Rd,pdMatrix.Rd,
2239 :     pdBlocked-class.Rd},AllClass.R,AllGeneric.R:
2240 :     Moved the pdMat classes from the lme4 package.
2241 :    
2242 :     2004-03-02 Douglas Bates <bates@stat.wisc.edu>
2243 :    
2244 :     * man/ssclme-class.Rd: Update definition and documentation of the
2245 :     ssclme class to include the DIsqrt slot.
2246 :    
2247 :     * src/ssclme.c (ssclme_deviance): Modify order of computation
2248 :     (much faster using dsyrk, a level 3 BLAS routine).
2249 :    
2250 :     * src/Makefile (SUBLIBS): Change definition (K. Hornik)
2251 :    
2252 :     2004-02-28 Douglas Bates <bates@stat.wisc.edu>
2253 :    
2254 :     * tests/ssclme.R: Modify the test to account for the permutation
2255 :     of the levels of the grouping factors.
2256 :    
2257 :     2004-02-23 Douglas Bates <bates@stat.wisc.edu>
2258 :    
2259 :     * R/ssclme.R,src/ssclme.c (ssclme): Move slots of sscCrosstab slot
2260 :     directly into the ssclme class definition.
2261 :    
2262 :     2004-02-22 Douglas Bates <bates@stat.wisc.edu>
2263 :    
2264 :     * DESCRIPTION (Date): New release
2265 :    
2266 :     * man/ssclme-class.Rd: new file.
2267 :    
2268 :     * src/ssclme.c (ssclme_loglik): major revisions in design. It
2269 :     works and it's fast!
2270 :    
2271 :     2004-02-17 Douglas Bates <bates@stat.wisc.edu>
2272 :    
2273 :     * src/taucs/Makefile.win (lib): Change "ar" to "$(AR)" (B.Ripley)
2274 :    
2275 :     2004-02-16 Douglas Bates <bates@stat.wisc.edu>
2276 :    
2277 :     * DESCRIPTION (Date): New release
2278 :    
2279 :     * NAMESPACE: Don't export ssclme.
2280 :    
2281 :     * data/ScotsSec.rda, man/ScotsSec.Rd: Add Scottish secondary
2282 :     school data.
2283 :    
2284 :     2004-02-11 Douglas Bates <bates@stat.wisc.edu>
2285 :    
2286 :     * src/sscCrosstab.c (sscCrosstab): Added a row to the incidence to
2287 :     keep track of the fixed-effects and the response. Counts also
2288 :     gets an extra element, which is always one.
2289 :    
2290 :     * src/ldl.c: Include these routines from Tim Davis' LDL package.
2291 :    
2292 :     2004-02-10 Douglas Bates <bates@stat.wisc.edu>
2293 :    
2294 :     * src/cscMatrix.c (csc_transpose): new function
2295 :    
2296 :     * src/Mutils.c (csc_sort_columns): perm/iperm confusion corrected
2297 :     (csc_components_transpose): new function
2298 :    
2299 :     2004-02-06 Douglas Bates <bates@stat.wisc.edu>
2300 :    
2301 :     * src/triplet.c (triplet_validate): Fix Dim slot on generated
2302 :     triplets
2303 :    
2304 :     2004-01-30 Douglas Bates <bates@stat.wisc.edu>
2305 :    
2306 :     * R/sscCrosstab.R (sscCrosstab): Added sscCrosstab generator function.
2307 :    
2308 :     * src/LU.h (MATRIX_LU_H): Add #ifndef #define ... #endif to this
2309 :     and all other .h files in src.
2310 :    
2311 :     * src/Makefile.win: This and other Makefile.win files contributed
2312 :     by Brian Ripley.
2313 :    
2314 :     2004-01-27 Douglas Bates <bates@stat.wisc.edu>
2315 :    
2316 :     * R/syMatrix.R: Added methods for "%*%".
2317 :    
2318 :     * R/Hilbert.R (Hilbert): Changed Hilbert function to return a
2319 :     poMatrix object.
2320 :    
2321 :     2004-01-26 Douglas Bates <bates@stat.wisc.edu>
2322 :    
2323 :     * man/sscChol-class.Rd,man/mm.Rd,man/y.Rd: Added man pages.
2324 :    
2325 :     2004-01-25 Douglas Bates <bates@bates2_home>
2326 :    
2327 :     * inst/doc/Introduction.Rnw,Comparisons.Rnw: Added vignettes.
2328 :    
2329 :     * R/csc.R: Convert all cscMatrix classes to use Dim slot instead
2330 :     of nrow.
2331 :    
2332 :     2003-12-31 Douglas Bates <bates@stat.wisc.edu>
2333 :    
2334 :     * src/taucs/taucs.h: Moved taucs.h, amd.h, and umfpack.h into
2335 :     subdirectories.
2336 :    
2337 :     2003-12-08 Douglas Bates <bates@stat.wisc.edu>
2338 :    
2339 :     * src/taucs.h: Accidently referred to global header files
2340 :     instead of local files.
2341 :    
2342 :     2003-12-04 Douglas Bates <bates@stat.wisc.edu>
2343 :    
2344 :     * R/AllClass.R: Lots of changes. Removed all the lapack++ code
2345 :     and methods and replaced all classes with S4 classes.
2346 :    
2347 :     2003-04-19 Douglas Bates <bates@stat.wisc.edu>
2348 :    
2349 :     * R/det.R,man/det.Rd: Change name of det generic to determinant
2350 :    
2351 :     * src/R_LapackPP.cc: Change method of calculating determinants
2352 :    
2353 :     2003-02-03 Douglas Bates <bates@stat.wisc.edu>
2354 :    
2355 :     * DESCRIPTION (Version): removed empty data directory as requested
2356 :     by CRAN maintainers. Changed version number and date.
2357 :    
2358 :     2002-10-23 Douglas Bates <bates@stat.wisc.edu>
2359 :    
2360 :     * src/laindex.h: Applied patches from Brian Ripley for compilation
2361 :     under Windows.
2362 :    
2363 :     * Added configure.win and src/Makevars.win as requested by Brian
2364 :     Ripley.
2365 :    
2366 :     2002-05-03 Douglas Bates <bates@stat.wisc.edu>
2367 :    
2368 :     * src/lamatrix.h: Removing pre-1.2.0 compatibility code per Kurt
2369 :     Hornik.
2370 :    
2371 :     2002-04-24 Douglas Bates <bates@stat.wisc.edu>
2372 :    
2373 :     * configure.ac: Replaced configure.in with configure.ac
2374 :     contributed by Kurt Hornik.
2375 :    
2376 :     * aclocal.m4 (ac_clean_files): Replaced this with Kurt Hornik's
2377 :     version for R-1.5.0
2378 :    
2379 : maechler 512
2380 : bates 10 2001-12-10 Douglas Bates <bates@stat.wisc.edu>
2381 :    
2382 :     * man/eigen.Rd: Removed the .Alias in the example

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