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1 :	maechler	2061	2007-08-30 Martin Maechler <maechler@stat.math.ethz.ch>
2 :
3 :			* src/Mutils.h (__sun): clause for alloca.h on Solaris
4 :
5 :	maechler	2056	2007-08-16 Martin Maechler <maechler@stat.math.ethz.ch>
6 :
7 :			* DESCRIPTION (Date, Version): 0.999375-2
8 :
9 :			2007-08-15 Martin Maechler <maechler@stat.math.ethz.ch>
10 :
11 :			* R/HBMM.R (readMM): make work for pattern matrices as well
12 :
13 :	bates	2050	2007-08-14 13:07 Douglas Bates <bates@stat.wisc.edu>
14 :
15 :			* [r4730] src/Mutils.h: declare alloca
16 :			* [r4734] NAMESPACE, R/AllGeneric.R, R/Csparse.R, R/HBMM.R, R/Tsparse.R,
17 :			R/dgCMatrix.R, R/dgTMatrix.R, R/dsCMatrix.R, R/dsTMatrix.R,
18 :			man/externalFormats.Rd, src/Csparse.c, src/Csparse.h, src/DEPS.mkf,
19 :			src/HBMM.c, src/HBMM.h, src/Mutils.h, src/SOURCES_C.mkf, src/init.c,
20 :			src/mmio.c, src/mmio.h: Remove deprecated function writeHB and its
21 :			methods; switch writeMM to use CHOLMOD code; repair readMM
22 :
23 :	maechler	2048	2007-08-14 Martin Maechler <maechler@stat.math.ethz.ch>
24 :
25 :			* R/nearPD.R, man/nearPD.Rd (nearPD): new function built on Jens
26 :			Oehlschlaegel's ... result type still to be discussed!
27 :
28 :	maechler	2043	2007-08-10 Martin Maechler <maechler@stat.math.ethz.ch>
29 :
30 :			* man/image-methods.Rd: new, combining all image() methods
31 :
32 :			2007-08-09 Martin Maechler <maechler@stat.math.ethz.ch>
33 :
34 :			* R/dgCMatrix.R: define qr() and lu() methods for "sparseMatrix"
35 :			to work via dgC...
36 :
37 :			* R/Matrix.R (Matrix): special treatment for "table" (S3)
38 :
39 :			2007-08-07 Martin Maechler <maechler@stat.math.ethz.ch>
40 :
41 :			* R/dgTMatrix.R (image): change defaults to
42 :			aspect = "iso", colorkey = FALSE
43 :
44 :	maechler	2039	2007-08-06 Martin Maechler <maechler@stat.math.ethz.ch>
45 :
46 :			* src/dsyMatrix.c (dsyMatrix_matrix_mm): 'b' might be matrix;
47 :			must copy its *expanded* x slot before LAPACK call.
48 :
49 :			* tests/matprod.R: test the last days' changes.
50 :
51 :	bates	2041	2007-08-06 16:43 Douglas Bates <bates@stat.wisc.edu>
52 :
53 :			* [r4712] inst/include/Matrix_stubs.c: Change R_cholmod_printf in stubs
54 :			as well as in sources
55 :	bates	2050	* [r4713] src/dsyMatrix.c: Duplicate the contents of the RHS before
56 :			Lapack call
57 :	maechler	2043
58 :	maechler	2036	2007-08-03 Martin Maechler <maechler@stat.math.ethz.ch>
59 :
60 :			* R/Matrix.R (%*%, crossprod, tcrossprod): add method for
61 :	maechler	2039	("Matrix", "matrix") which is needed in some cases.
62 :			Ditto for solve().
63 :	maechler	2036
64 :			* R/colSums.R (.as.dge.Fun): need ddenseMatrix methods to avoid
65 :			infinite recursion in dispatch for some cases.
66 :
67 :	bates	2041	2007-08-02 08:48 Martin Maechler <maechler@stat.math.ethz.ch>
68 :	maechler	2036
69 :	bates	2041	* [r4693] src/chm_common.c: R_cholmod_printf() instead of Rprintf() just
70 :			so pointers match
71 :
72 :	maechler	2024	2007-08-02 Martin Maechler <maechler@stat.math.ethz.ch>
73 :
74 :	maechler	2036	* DESCRIPTION (Date): set ready for release -- 0.999375-1
75 :	maechler	2024
76 :	bates	2020	2007-08-01 15:44 Douglas Bates <bates@stat.wisc.edu>
77 :
78 :			* [r4686] inst/include/Matrix.h, inst/include/Matrix_stubs.c,
79 :			src/chm_common.c, src/chm_common.h: Change API for
80 :			numeric_as_chm_dense and N_AS_CHM_DN
81 :	maechler	2024
82 :	maechler	2018	2007-08-01 Martin Maechler <maechler@stat.math.ethz.ch>
83 :
84 :			* src/dtrMatrix.c (dtrMatrix_matrix_mm): fix dimensionality check (!)
85 :			* tests/matprod.R: regr.test for it
86 :
87 :	maechler	2011	2007-07-20 Martin Maechler <maechler@stat.math.ethz.ch>
88 :
89 :			* R/dMatrix.R: fix from Brian for Math2(., digits = "missing")
90 :			* tests/group-methods.R: and regression-test it
91 :
92 :	bates	2008	2007-07-19 19:45 Douglas Bates <bates@stat.wisc.edu>
93 :
94 :			* [r4642] inst/include/Matrix.h, inst/include/Matrix_stubs.c,
95 :			inst/include/cholmod.h, src/chm_common.c, src/init.c: Export
96 :			triplet_to_sparse, documentation, use typedefs
97 :	maechler	2011
98 :	maechler	2005	2007-07-18 Martin Maechler <maechler@stat.math.ethz.ch>
99 :
100 :			* man/dpoMatrix-class.Rd: added 'corMatrix' example
101 :
102 :			* src/dsyMatrix.[ch] (dsyMatrix_as_matrix): new 'keep_dimnames' arg
103 :			* src/dtrMatrix.[ch] (dtrMatrix_as_matrix): ditto
104 :			* src/init.c, R/dsyMatrix.R, R/dtrMatrix.R, R/lgTMatrix.R: ditto
105 :
106 :			* R/lsparseMatrix.R: bug fix in "all" method
107 :			* R/Ops.R (.do.Logic.lsparse): "|" bug in borderline case
108 :
109 :			* R/dsyMatrix.R (coerce->dsTMatrix): (i,j) slots should *not* have names
110 :			* R/ngTMatrix.R (coerce->ngTMatrix): ditto;
111 :			+ matrix |-> nMatrix coercion
112 :			* R/pMatrix.R: + setAs() to dMatrix and from nMatrix
113 :			* man/pMatrix-class.Rd: ditto
114 :
115 :			* R/Matrix.R (Summary): method for non-dMatrix
116 :
117 :			* tests/Class+Meth.R (extraValid): new check about "dirty" slots
118 :			* tests/Class+Meth.R (tstMatrixClass): test norm(.);
119 :			test all Summary methods.
120 :
121 :			2007-07-16 Martin Maechler <maechler@stat.math.ethz.ch>
122 :
123 :			* R/dgeMatrix.R (norm, rcond): methods for 'matrix'
124 :
125 :			2007-07-14 Martin Maechler <maechler@stat.math.ethz.ch>
126 :
127 :			* R/sparseMatrix.R (norm): simple methods for sparseMatrix
128 :
129 :			* R/pMatrix.R (t?crossprod): methods for pMatrix
130 :
131 :	bates	1987	2007-07-10 Douglas Bates <bates@stat.wisc.edu>
132 :
133 :			* src/dgeMatrix.c (dgeMatrix_colsums): Get the logic straight.
134 :
135 :	bates	1975	2007-07-09 20:45 Douglas Bates <bates@stat.wisc.edu>
136 :
137 :			* [r4579] src/dgeMatrix.c: Untangle horrible code in dgeMatrix_colsums
138 :	maechler	2005	trying to fix a subtle bug - which has been somewhere else.
139 :	bates	1975
140 :			2007-07-09 19:43 Martin Maechler <maechler@stat.math.ethz.ch>
141 :
142 :			* [r4578] src/dgeMatrix.c: "cleaned" dgeMatrix_colsums() - but did not
143 :			solve the bug
144 :
145 :	maechler	1968	2007-07-08 Martin Maechler <maechler@stat.math.ethz.ch>
146 :	bates	1964
147 :	maechler	1968	* src/dgCMatrix.c (compressed_to_TMatrix):
148 :
149 :			2007-07-07 Martin Maechler <maechler@stat.math.ethz.ch>
150 :
151 :			* src/Csparse.c (Rsparse_validate): new, to have some validity
152 :			checking for RsparseMatrix
153 :			* src/dgCMatrix.c (xRMatrix_validate): ditto
154 :			* src/dtCMatrix.c (tRMatrix_validate): ditto
155 :
156 :			2007-07-07 Douglas Bates <bates@stat.wisc.edu>
157 :
158 :	bates	1964	* [r4567] R/AllClass.R: Slots already in RsparseMatrix were redefined in
159 :			lgRMatrix
160 :			* [r4568] DESCRIPTION: Prepare for bug-fix release
161 :	bates	1966	* [r4570] src/CHOLMOD/Check/cholmod_write.c: Include cholmod_matrixops.h
162 :			for declaration of cholmod_symmetry
163 :	maechler	1968
164 :	maechler	1961	2007-07-06 Martin Maechler <maechler@stat.math.ethz.ch>
165 :
166 :			* DESCRIPTION (Version): 0.999375 merged into the trunk; ready for
167 :			release.
168 :
169 :	maechler	1960	2007-07-06 14:11 Douglas Bates <bates@stat.wisc.edu>
170 :
171 :			* [r4559] src/iohb.c, src/iohb.h: Remove Harwell-Boeing input/output
172 :			functions - no longer used
173 :			* [r4560] src/HBMM.c, src/Mutils.c, src/dgTMatrix.c, src/dgeMatrix.c,
174 :			src/dspMatrix.c, src/dsyMatrix.c, src/dtCMatrix.c,
175 :			src/factorizations.c, src/sparseQR.c: Replace most calls to Calloc by
176 :			Alloca
177 :
178 :			2007-07-06 13:14 Martin Maechler <maechler@stat.math.ethz.ch>
179 :
180 :			* [r4558] inst/doc/Comparisons.Rnw, src/CHMfactor.c, src/Csparse.c,
181 :			src/Tsparse.c, src/chm_common.c, src/chm_common.h, src/dense.c,
182 :			src/dgCMatrix.c, src/dsCMatrix.c, src/dtTMatrix.c, src/sparseQR.c,
183 :			src/t_gCMatrix_colSums.c: more R_CheckStack()s
184 :
185 :			2007-07-05 18:12 Douglas Bates <bates@stat.wisc.edu>
186 :
187 :			* [r4550] inst/include/Matrix.h: Add the macro N_AS_CHM_DN to "alloca"
188 :			the required amount of memory then call M_numeric_as_chm_dense.
189 :			* [r4556] src/Mutils.h, src/dgCMatrix.c: Define and use the Alloca macro
190 :			(like Calloc but calling alloca)
191 :
192 :	maechler	1947	2007-07-05 Martin Maechler <maechler@stat.math.ethz.ch>
193 :
194 :			* R/sparseMatrix.R (printSpMatrix): renamed from prSpMatrix()
195 :			and extended with more sophisticated 'col.names' option.
196 :			* NAMESPACE: export printSparseMatrix()
197 :			* man/printSpMatrix.Rd: document, incl. examples
198 :
199 :	maechler	1960	2007-07-04 16:21 Douglas Bates <bates@stat.wisc.edu>
200 :
201 :			* [r4543] src/cs_utils.c, src/cs_utils.h, src/dgCMatrix.c,
202 :			src/dtCMatrix.c, src/sparseQR.c: CSP typedef for *cs and macro
203 :			AS_CSP. API change - pass the empty structure to Matrix_as_cs.
204 :
205 :	maechler	1945	2007-07-04 Martin Maechler <maechler@stat.math.ethz.ch>
206 :
207 :			* DESCRIPTION (Version): 0.99875-4
208 :
209 :			* tests/Class+Meth.R (tstMatrixClass): add dimnames, and hence test
210 :			some dimnames perservation.
211 :
212 :			* R/dsTMatrix.R (t-method): keep dimnames
213 :			* R/dtTMatrix.R: ditto
214 :
215 :			* R/sparseMatrix.R (prSpMatrix): print colnames when non-trivial
216 :			and ncol(.) < 10
217 :
218 :			* src/cs_utils.c: drop check_class() and use Matrix_check_class()
219 :			from Mutils.h
220 :
221 :			* src/lgCMatrix.c ([ln]csc_to_matrix): no longer lose dimnames,
222 :			e.g. in as(<ngCMatrix>, "matrix")
223 :
224 :	maechler	1960	2007-07-01 13:27 Douglas Bates <bates@stat.wisc.edu>
225 :
226 :			* [r4529] .: Create a branch for the API changes from the 0.99875
227 :			series to the 0.999375 series
228 :			* [r4530] DESCRIPTION, inst/include/Matrix.h,
229 :			inst/include/Matrix_stubs.c, src/CHMfactor.c, src/Csparse.c,
230 :			src/Mutils.h, src/Tsparse.c, src/chm_common.c, src/chm_common.h,
231 :			src/dense.c, src/dgCMatrix.c, src/dsCMatrix.c, src/dtTMatrix.c,
232 :			src/t_gCMatrix_colSums.c: API change - pass the empty structure to the
233 :			as_cholmod_x functions
234 :
235 :			2007-06-30 09:05 Martin Maechler <maechler@stat.math.ethz.ch>
236 :
237 :			* [r4527] trunk/Matrix/DESCRIPTION, trunk/Matrix/NAMESPACE,
238 :			trunk/Matrix/inst/doc/Comparisons.Rnw: add session- and hardware-info
239 :			to Comparisons
240 :
241 :			>>>>>>> .merge-right.r4561
242 :	maechler	1932	2007-06-29 Martin Maechler <maechler@stat.math.ethz.ch>
243 :
244 :			* DESCRIPTION (Version): 0.99875-3 ready to be released.
245 :
246 :			* R/sparseMatrix.R (spMatrix): make spMatrix(3,4) working
247 :
248 :			* R/AllGeneric.R: set "Math" (and "Math2") group generics in a way
249 :			that should also work in a future version of R.
250 :
251 :	maechler	1922	2007-06-21 Martin Maechler <maechler@stat.math.ethz.ch>
252 :
253 :			* NAMESPACE, R/AllClass.R: "xsparseVector" class union.
254 :
255 :			* R/sparseVector.R: more *sparseVector coercions, notably for
256 :			non - double ones.
257 :
258 :	maechler	1911	2007-06-19 Martin Maechler <maechler@stat.math.ethz.ch>
259 :
260 :			* R/colSums.R: new file for all (col|row)(Sums|Means) methods,
261 :			notably the new ones building on the new .Call(.)s:
262 :
263 :			* src/dgCMatrix.c (DEF_gCMatrix_COLSUMS): use to define
264 :			all 4 of [dlin]gCMatrix_colSums().
265 :
266 :	bates	1909	2007-06-18 16:12 Douglas Bates <bates@stat.wisc.edu>
267 :
268 :			* [r4472] src/Syms.h, src/init.c: Added Matrix_lengthSym
269 :			* [r4473] src/dgCMatrix.c: Modified dgCMatrix_colSums for sparseVector
270 :			result
271 :	maechler	1911
272 :	maechler	1903	2007-06-16 Martin Maechler <maechler@stat.math.ethz.ch>
273 :
274 :	maechler	1904	* R/kronecker.R: fix typo (could lead to inf.recursion)
275 :			* test/simple.R: testing that
276 :
277 :	maechler	1903	* R/sparseMatrix.R (prSpMatrix): change to be used as print()
278 :	maechler	1922	method as well (which can have arguments, show() can't).
279 :	maechler	1903
280 :	bates	1902	2007-06-16 15:52 Douglas Bates <bates@stat.wisc.edu>
281 :
282 :			* [r4466] R/dgCMatrix.R, src/dgCMatrix.c, src/dgCMatrix.h, src/init.c:
283 :			added dgCMatrix_colSums for [col,row][Sums,Means]
284 :
285 :	bates	1899	2007-06-15 23:15 Douglas Bates <bates@stat.wisc.edu>
286 :	bates	1897
287 :			* [r4460] R/sparseMatrix.R, man/dgCMatrix-class.Rd, src/dgCMatrix.c,
288 :			src/dgCMatrix.h, src/init.c: added lm.fit.sparse (unexported),
289 :			coercion of "factor" to "dgCMatrix" and dgCMatrix_cholsol
290 :			* [r4461] R/AllClass.R, man/sparseMatrix-class.Rd: draft "indicators"
291 :			class
292 :	bates	1899	* [r4463] R/sparseMatrix.R, man/dgCMatrix-class.Rd,
293 :			man/sparseMatrix-class.Rd: Don't need an "indicators" class - use the
294 :			row names to store the levels - duh! Added an example.
295 :	maechler	1903
296 :	maechler	1893	2007-06-14 Martin Maechler <maechler@stat.math.ethz.ch>
297 :
298 :			* src/Csparse.c (Csparse_validate): check for *repeated* entries
299 :			thanks to example from Christian Buchta; with a test here:
300 :			* tests/simple.R:
301 :
302 :	maechler	1886	2007-06-07 Martin Maechler <maechler@stat.math.ethz.ch>
303 :
304 :			* R/Auxiliaries.R (callGeneric): another fix, needed for some cases
305 :			of colSums(*, sparseResult = TRUE)
306 :
307 :	maechler	1883	2007-06-06 Martin Maechler <maechler@stat.math.ethz.ch>
308 :
309 :			* R/lsparseMatrix.R, R/ldenseMatrix.R (all, any): change default to
310 :			'na.rm = FALSE' as "everywhere" else in R.
311 :
312 :	bates	1877	2007-06-05 Douglas Bates <bates@stat.wisc.edu>
313 :
314 :	bates	1878	* [r4421] src/CSparse_install.sh: Modify for new organization of
315 :	maechler	1883	CSparse package
316 :	bates	1877	* [r4425] src/UFsparse_download.sh: Update to version 3.0.0 of
317 :			SuiteSparse
318 :			* [r4426] src/Makefile: add ./UFconfig to the include path for
319 :			compilation
320 :	maechler	1883	* [r4427] src/cs.[ch]: update to CSparse version 2.2.0
321 :			* [r4428] inst/doc/UFsparse/* src/{AMD,CHOLMOD,COLAMD}/*
322 :			src/UFconfig/UFconfig.h: Update to version 3.0.0 of SuiteSparse
323 :
324 :	maechler	1870	2007-06-05 Martin Maechler <maechler@stat.math.ethz.ch>
325 :
326 :			* R/Auxiliaries.R (emptyColnames): + argument msg.if.not.empty, used in
327 :			* R/sparseMatrix.R (prSpMatrix): now gives a message about
328 :			suppressed column names.
329 :
330 :	bates	1868	2007-06-04 17:13 Douglas Bates <bates@stat.wisc.edu>
331 :
332 :			* [r4418] src/Csparse.c, src/HBMM.c, src/Mutils.c, src/Mutils.h,
333 :			src/Tsparse.c, src/chm_common.c, src/chm_common.h, src/dgCMatrix.c,
334 :			src/dgeMatrix.c, src/dpoMatrix.c, src/dpoMatrix.h, src/dppMatrix.c,
335 :			src/dppMatrix.h, src/dsCMatrix.c, src/dspMatrix.c, src/dspMatrix.h,
336 :			src/dsyMatrix.c, src/dsyMatrix.h, src/dtpMatrix.c, src/dtrMatrix.c:
337 :			Remove warnings after change to const char* CHAR
338 :
339 :			2007-06-04 17:11 Douglas Bates <bates@stat.wisc.edu>
340 :
341 :			* [r4417] inst/include/Matrix_stubs.c, inst/include/cholmod.h: Corrected
342 :			type of M_cholmod_ssmult
343 :
344 :	bates	1863	2007-06-03 14:42 Douglas Bates <bates@stat.wisc.edu>
345 :
346 :			* [r4412] inst/include/Matrix_stubs.c, inst/include/cholmod.h,
347 :			src/init.c: Yet another cholmod export - cholmod_ssmult
348 :
349 :	maechler	1855	2007-05-23 Martin Maechler <maechler@stat.math.ethz.ch>
350 :
351 :			* NAMESPACE: exported drop0(), since
352 :			* man/drop0.Rd: I have seen several cases, I really wanted to use
353 :			it, so our users may want too.
354 :
355 :			2007-05-22 Martin Maechler <maechler@stat.math.ethz.ch>
356 :
357 :			* man/colSums.Rd: separately document colSums() etc, since these
358 :			have the extra argument 'sparseResult'.
359 :
360 :	maechler	1852	2007-05-21 Martin Maechler <maechler@stat.math.ethz.ch>
361 :
362 :			* R/sparseMatrix.R (spMatrix): utility (T)sparse Matrix constructor;
363 :			* man/spMatrix.Rd: docu., including examples
364 :
365 :			* R/Auxiliaries.R (sp.colMeans): etc, using a patched callGeneric(),
366 :			in order to make colMeans() etc fast *and* correct.
367 :			* R/sparseVector.R (replSPvec): "[<-" functionality for
368 :			sparseVectors; tested in
369 :			* tests/simple.R:
370 :
371 :			2007-05-19 Martin Maechler <maechler@stat.math.ethz.ch>
372 :
373 :			* R/sparseMatrix.R (print.sparseSummary): and summary() method for
374 :			(very) sparse Matrices; output similar to Matlab's print().
375 :
376 :	bates	1847	2007-05-17 Douglas Bates <bates@stat.wisc.edu>
377 :
378 :			* src/HBMM.c (Matrix_writeMatrixMarket): Write 1-based, not
379 :			0-based, indices (Jose Quesada <quesada@gmail.com>).
380 :
381 :	bates	1844	2007-05-16 Douglas Bates <bates@stat.wisc.edu>
382 :
383 :			* R/CHMfactor.R: Added solve methods for a CHMfactor object.
384 :
385 :	maechler	1845	2007-05-16 Martin Maechler <maechler@stat.math.ethz.ch>
386 :
387 :			* R/Auxiliaries.R (sparsapply): new utility, much faster than
388 :			tapply1() for large sparse matrices.
389 :
390 :			2007-05-15 Martin Maechler <maechler@stat.math.ethz.ch>
391 :
392 :			* R/Matrix.R (dim<-): reshape now via sparseVector.
393 :
394 :			* R/sparseVector.R: methods and function for
395 :			* R/AllClass.R: new "sparseVector" class and daughters.
396 :			* NAMESPACE: export new classes
397 :
398 :	maechler	1837	2007-05-14 Martin Maechler <maechler@stat.math.ethz.ch>
399 :
400 :			* DESCRIPTION (Version): 0.99875-1
401 :			* src/Makefile.win: also remove Lapack code from here (cf. 04-25).
402 :
403 :	maechler	1834	2007-05-11 Martin Maechler <maechler@stat.math.ethz.ch>
404 :
405 :			* R/Tsparse.R ([, Tsparse): fix last case: *duplicated*, symmetric
406 :			indexing
407 :			* tests/indexing.R: test set for that.
408 :
409 :	maechler	1833	2007-05-08 Martin Maechler <maechler@stat.math.ethz.ch>
410 :
411 :			* R/Tsparse.R (replTmat): fix the case of *duplicated* index
412 :			entries.
413 :			* tests/indexing.R(out): add regression test for it
414 :
415 :			2007-04-30 Martin Maechler <maechler@stat.math.ethz.ch>
416 :
417 :			* R/(l(dense|sparse))?Matrix.R (!): use 'x', not 'e1' as argument
418 :			name for "!" method definitions.
419 :
420 :	maechler	1829	2007-04-26 Martin Maechler <maechler@stat.math.ethz.ch>
421 :
422 :			* R/Tsparse.R (intI): new utility, used for "[" :
423 :			Cleanup up there, and fixes for duplicated indices - more TODO!
424 :
425 :			* tests/indexing.R(out): more tests
426 :
427 :	bates	1827	2007-04-25 Douglas Bates <bates@stat.wisc.edu>
428 :
429 :			* DESCRIPTION,src/Makefile: require R>= 2.5.0 and remove Lapack
430 :			code that is now part of the R Lapack library.
431 :	maechler	1829
432 :	bates	1827	* src/init.c,inst/include/{Matrix_stubs.c,cholmod.h}:export
433 :			cholmod_factorize_p (used in lme4 for GLMMs and NLMMs).
434 :
435 :	maechler	1829	2007-04-21 Martin Maechler <maechler@stat.math.ethz.ch>
436 :
437 :			* R/Matrix.R (image): method for all Matrices, not just sparse ones.
438 :
439 :			2007-04-17 Martin Maechler <maechler@stat.math.ethz.ch>
440 :
441 :			* R/Auxiliaries.R (tapply1): unname(.) -> colSums() etc don't end
442 :			up with extraneous names '0'...'<n-1>'
443 :
444 :	maechler	1825	2007-04-12 Martin Maechler <maechler@stat.math.ethz.ch>
445 :
446 :			* R/dgTMatrix.R (mat2dgT): care about NAs
447 :
448 :			2007-04-11 Martin Maechler <maechler@stat.math.ethz.ch>
449 :
450 :			* R/kronecker.R: triangularity preserving methods
451 :
452 :	maechler	1803	2007-03-27 Martin Maechler <maechler@stat.math.ethz.ch>
453 :
454 :			* R/kronecker.R: new file collecting kronecker() methods in one
455 :			place. Goal: become much faster!
456 :
457 :	maechler	1799	2007-03-23 Martin Maechler <maechler@stat.math.ethz.ch>
458 :
459 :			* src/dtCMatrix.c (dtCMatrix_solve): use the new code from Kasper
460 :			Kristensen based cs_spsolve() instead of _lsolve & _usolve which
461 :			can be much faster.
462 :
463 :			* tests/matprod.R: add regression tests for these (upper & lower).
464 :
465 :			2007-03-19 Martin Maechler <maechler@stat.math.ethz.ch>
466 :
467 :			* R/Matrix.R (diff): method for our Matrices.
468 :
469 :			* R/sparseMatrix.R (isDiagonal): check dim()!
470 :
471 :			2007-03-17 Martin Maechler <maechler@stat.math.ethz.ch>
472 :
473 :			* R/Matrix.R (dim<-): new method for "reshape()" built on a
474 :			proposal from Tamas Papp.
475 :
476 :			2007-03-16 Martin Maechler <maechler@stat.math.ethz.ch>
477 :
478 :			* R/AllGeneric.R: remove all if(!isGeneric(.)) clauses
479 :
480 :			* R/zzz.R (.onLoad, .onUnload): do *not* leave bind_activation(TRUE);
481 :	maechler	1803	rather define and export cBind() and rBind() only.
482 :			--> useRs *must* change code that used to have cbind()/rbind() !!
483 :	maechler	1799
484 :	maechler	1803	* R/bind.R: change tests from cbind() to cBind() and similarly to rBind()
485 :			* R/bind.Rout.save: ditto
486 :	maechler	1799
487 :	bates	1787	2007-02-16 Douglas Bates <bates@r-project.org>
488 :
489 :			* DESCRIPTION (Date, Version): 0.9975-11 with new date
490 :			* src/dgCMatrix.c (R_to_CMatrix, compressed_to_TMatrix): remove
491 :			const modifier on declaration of the array 'valid'
492 :
493 :	bates	1786	2007-02-12 Douglas Bates <bates@stat.wisc.edu>
494 :
495 :			* R/CHMfactor.R: Add image method (coercion to sparseMatrix).
496 :
497 :	maechler	1765	2007-02-05 Martin Maechler <maechler@stat.math.ethz.ch>
498 :
499 :	maechler	1768	* DESCRIPTION (Date, Version): 0.9975-10 with new date.
500 :
501 :	maechler	1767	* R/Ops.R (Arith): make sure Csparse o Csparse also works for e.g. ntCMatrix
502 :			* tests/simple.R: test the above and some of these coercions:
503 :
504 :			* R/nsparseMatrix.R: coercing "Csparse" to "lsparseMatrix";
505 :			be careful to avoid infinite recursion, using new coercions in
506 :			* R/ngCMatrix.R and nsC... and ntC...
507 :			* R/lsparseMatrix.R: ditto
508 :
509 :	maechler	1765	* R/SparseM-conv.R: more conversion, notably for triplet matrices.
510 :
511 :	maechler	1767	* src/dgCMatrix.c (R_to_C_Matrix): port Doug's fix and
512 :			* R/Rsparse.R: reactivate .Call()s
513 :	maechler	1765
514 :	maechler	1767	* tests/Class+Meth.R: a bit more on actual classes
515 :
516 :			2007-02-04 Douglas Bates <bates@stat.wisc.edu>
517 :
518 :			* src/dgCMatrix.c (compressed_to_TMatrix): fix memory bug using strdup()
519 :
520 :	maechler	1760	2007-02-03 Martin Maechler <maechler@stat.math.ethz.ch>
521 :	maechler	1758
522 :			* DESCRIPTION (Version): 0.9975-10 to upload
523 :
524 :	maechler	1760	* tests/Class+Meth.R (tstMatrixClass): require coercions to
525 :			specific classes less unconditionally.
526 :
527 :			* R/Auxiliaries.R: get rid of as_Tsparse() and as_Rsparse()
528 :
529 :			* R/Tsparse.R (triu): etc, use as(*, "TsparseMatrix") instead of as_Tsparse()
530 :
531 :			* R/Rsparse.R (.R.2.T): R-level workaround using compressed_to_TMatrix.
532 :	maechler	1758	* R/Rsparse.R (.R.2.C): R-level workaround since C-level
533 :			R_to_CMatrix segfaults on one platform.
534 :	maechler	1760	Eliminate most coercion method to *specific* classes, and replace
535 :			with virtual classes coercions.
536 :	maechler	1758
537 :	maechler	1760
538 :	maechler	1758	2007-02-01 Martin Maechler <maechler@stat.math.ethz.ch>
539 :
540 :			* src/init.c: export the CHM...._validate() placeholders, since
541 :			they *are* called.
542 :
543 :	maechler	1760	* tests/Class+Meth.R (classCanCoerce): and starting to test
544 :	maechler	1758	all as(<from>, <to>)
545 :
546 :	maechler	1751	2007-01-30 Martin Maechler <maechler@stat.math.ethz.ch>
547 :
548 :			* R/Tsparse.R ([): more care when subsetting triangular Tsparse
549 :			* tests/indexing.R: tested now
550 :			* tests/indexing.Rout.save: updated
551 :
552 :			* src/Csparse.c (Csparse_to_dense): use Rkind = -1 for PATTERN to
553 :			* src/chm_common.c (chm_dense_to_SEXP): return "ngeMatrix" when
554 :			appropriate.
555 :
556 :			* NAMESPACE: export a trivial
557 :			* R/Matrix.R: drop() Matrix-method
558 :
559 :			* R/AllClass.R: moved all prototypes to virtual super classes.
560 :
561 :			* R/Rsparse.R: many more coercions to have less exceptions in
562 :			* tests/Class+Meth.R:
563 :
564 :			* R/Ops.R (Compare): tweak for case with NA
565 :			* tests/simpl.R: hence another 'FIXME' eliminated
566 :
567 :	maechler	1747	2007-01-29 Martin Maechler <maechler@stat.math.ethz.ch>
568 :
569 :	maechler	1748	* R/diagMatrix.R (solve): the obvious methods for diagonalMatrix
570 :			objects.
571 :
572 :	maechler	1747	* tests/Class+Meth.R (tstMatrixClass): now testing diag(), nnzero(),
573 :			and more of "!", "&", "|", all, any; coercions
574 :
575 :			* R/Rsparse.R: many coercions (which enable quite a few other
576 :			methods), thanks to enhancements in
577 :			* src/dgCMatrix.c (R_to_CMatrix): new, and
578 :			* src/dgCMatrix.c (compressed_to_TMatrix): now for (d,l,n) ,
579 :			symmetric & triangular and ..RMatrix objects.
580 :
581 :			* src/TMatrix_as.c (Matrix_T_as_DENSE,Matrix_T_as_GENERAL):
582 :			renamed file from src/dsTMatrix.c;
583 :			now dealing with symmetric and triangular Tsparse coercions, both
584 :			to dense and general.
585 :
586 :			2007-01-27 Martin Maechler <maechler@stat.math.ethz.ch>
587 :
588 :			* src/dsTMatrix.c: has now "l" and "n" methods besides the "d" ones.
589 :
590 :			* R/Ops.R (Arith): <dgCMatrix> o <numeric> now remains sparse
591 :			where sensible when the <numeric> is of length > 1.
592 :
593 :			2007-01-26 Martin Maechler <maechler@stat.math.ethz.ch>
594 :
595 :			* R/Matrix.R ([<-): for M[] <- value: fix length
596 :
597 :			2007-01-25 Martin Maechler <maechler@stat.math.ethz.ch>
598 :
599 :			* R/Auxiliaries.R (n2l_Matrix): new, to be used in
600 :			* R/ndenseMatrix.R: new coercions n* -> l*
601 :
602 :	maechler	1738	2007-01-22 Martin Maechler <maechler@stat.math.ethz.ch>
603 :
604 :			* R/triangularMatrix.R: new file; simple triu() and tril() methods.
605 :
606 :			* R/Ops.R ("Logic"): and other "Ops", many updates
607 :
608 :			2007-01-18 Martin Maechler <maechler@stat.math.ethz.ch>
609 :
610 :			* src/Mutils.h (SET_DimNames): new utility
611 :
612 :			* R/Auxiliaries.R (nnzero): improved and now exported via
613 :
614 :			* NAMESPACE: + nnzero(); length() == prod(dim(.)) method for all "Matrix" objects
615 :
616 :	maechler	1725	2007-01-17 Martin Maechler <maechler@stat.math.ethz.ch>
617 :
618 :			* R/diagMatrix.R (!): fix typo.
619 :
620 :			2007-01-16 Martin Maechler <maechler@stat.math.ethz.ch>
621 :
622 :			* R/Auxiliaries.R (as_Csparse): and quite a few others:
623 :			allow to pass class definition --> speedup
624 :			* R/sparseMatrix.R: apply the above
625 :
626 :			* R/Csparse.R: coercion Csparse* to dense* now preserves shape properties.
627 :
628 :			* src/Mutils.h (mMatrix_as_geMatrix): new, based on
629 :			* src/Mutils.c (dup_mMatrix_as_geMatrix): new; generalization of
630 :			old dup_mMatrix_as_dgeMatrix), eliminating a long-standing "FIXME".
631 :
632 :			* src/dense.c (dense_to_Csparse): use new mMatrix_as_geMatrix()
633 :
634 :			* R/denseMatrix.R (.dense2C): based on dense_to_Csparse: name it,
635 :			and use it for "sparse*" as well, since it's faster than the
636 :			as_Csparse(.) way.
637 :
638 :			2007-01-15 Martin Maechler <maechler@stat.math.ethz.ch>
639 :
640 :			* R/Ops.R ("Logic"): more methods, notably an <lgC> o <lgC> one.
641 :
642 :	maechler	1724	2007-01-12 Martin Maechler <maechler@stat.math.ethz.ch>
643 :
644 :			* R/Tsparse.R (.TM.repl.i.2col): new internal function to be used
645 :			as method for M[ ij ] <- v
646 :			* R/Csparse.R:: go via Tsparse for "M[ij] <- v"
647 :
648 :			* R/Ops.R: "Compare" for (C|R)sparse: need pointer slot for all
649 :			FALSE answer
650 :
651 :			* R/Csparse.R (replCmat): fix the "all non-zero" case with reordering
652 :			* tests/indexing.R: test it, and some of the above
653 :
654 :			2007-01-05 Martin Maechler <maechler@stat.math.ethz.ch>
655 :
656 :			* R/Auxiliaries.R (is_duplicatedT): new utility
657 :
658 :	bates	1716	2007-01-05 Douglas Bates <bates@stat.wisc.edu>
659 :
660 :			* src/init.c (R_init_Matrix): export cholmod_scale
661 :
662 :	maechler	1724	2006-12-30 Martin Maechler <maechler@stat.math.ethz.ch>
663 :
664 :			* R/zzz.R (tmp): for R >= 2.5.0, extend formals of our
665 :			base::as.matrix to (x, ...)
666 :
667 :	maechler	1714	2006-12-28 Martin Maechler <maechler@stat.math.ethz.ch>
668 :
669 :			* R/Ops.R ("Arith" etc): move almost all "Ops" methods to new R
670 :			file; start using "Logic", hence
671 :
672 :			* DESCRIPTION (Depends): R >= 2.4.1 (since we want "Logic")
673 :			* NAMESPACE: import and export "Logic"
674 :
675 :			2006-12-27 Martin Maechler <maechler@stat.math.ethz.ch>
676 :
677 :			* src/zpotfr.f and dependencies: use LAPACK 3.1 version
678 :			only needed previously to R version 2.5.0.
679 :	maechler	1724
680 :	maechler	1710	2006-12-26 Martin Maechler <maechler@stat.math.ethz.ch>
681 :
682 :			* DESCRIPTION (Date, Version): 0.9975-8, ready for release
683 :
684 :			* R/Tsparse.R (replTmat): fix subassignment of triangular
685 :			* R/Csparse.R (replCmat): ditto
686 :			* tests/indexing.R: more tests, incl the above fix
687 :
688 :			2006-12-23 Martin Maechler <maechler@stat.math.ethz.ch>
689 :
690 :			* R/Auxiliaries.R (drop0): extend for non CSparse
691 :			* R/Auxiliaries.R (diagU2N): should work for all sparseMatrix
692 :
693 :			* src/Csparse.c (Csparse_to_Tsparse, Csparse_general_to_symmetric):
694 :			use uplo correctly (!); other places: use uplo_P() macro
695 :
696 :			* R/Csparse.R (replCmat): call diagU2N() when needed
697 :			* R/Tsparse.R (replTmat): ditto
698 :
699 :			* src/dtCMatrix.c (tCMatrix_validate): new
700 :			* src/dtTMatrix.c (tTMatrix_validate): new, used in
701 :			* R/AllClass.R: for validity of dtC, dsC, and dtT, dsT.
702 :
703 :			* R/diagMatrix.R (replDiag): to use in [<-
704 :
705 :	maechler	1708	2006-12-22 Martin Maechler <maechler@stat.math.ethz.ch>
706 :
707 :			* R/Auxiliaries.R (as_Csparse2, as_geSimpl): new functions;
708 :			also more general diagU2N().
709 :
710 :			2006-12-21 Martin Maechler <maechler@stat.math.ethz.ch>
711 :
712 :			* R/bind2.R: new file for all cbind2(), rbind() methods moved here
713 :			from R/<foo>Matrix.R files. Better diagonal & improved sparse methods.
714 :
715 :	maechler	1707	2006-12-20 Martin Maechler <maechler@stat.math.ethz.ch>
716 :
717 :			* tests/bind.R: a few more cases
718 :			* R/Auxiliaries.R (.M.kind): also work for atomic vectors
719 :
720 :			* R/denseMatrix.R (cbind2/rbind2): moved here (and generalized) from
721 :			* R/ddenseMatrix.R (cbind2/rbind2)
722 :			* R/Tsparse.R (replTmat): final(?!) fix for "[<-" ..
723 :			* tests/indexing.R
724 :			* tests/indexing.Rout.save: updated
725 :
726 :			2006-12-18 Martin Maechler <maechler@stat.math.ethz.ch>
727 :
728 :			* R/Tsparse.R (replTmat): fixed a remaining "[<-" bug in
729 :			* tests/indexing.R
730 :
731 :	maechler	1705	2006-12-15 Martin Maechler <maechler@stat.math.ethz.ch>
732 :
733 :			* R/sparseMatrix.R (prSpMatrix): "." alignment much improved:
734 :			align with proper position of "0", i.e., right for integers.
735 :			argument 'align' by default is "fancy".
736 :
737 :			2006-12-14 Martin Maechler <maechler@stat.math.ethz.ch>
738 :
739 :			* R/sparseMatrix.R: delegate "Compare" to "Csparse.."
740 :			* R/Csparse.R: and fix "Compare" for more cases.
741 :			* tests/Class+Meth.R: test some of these (m == m, m != m)
742 :
743 :			2006-12-13 Martin Maechler <maechler@stat.math.ethz.ch>
744 :
745 :			* R/lsparseMatrix.R: all() and any() methods
746 :			* R/ldenseMatrix.R: ditto
747 :			* NAMESPACE, R/Matrix.R: ditto
748 :
749 :			* man/all-methods.Rd: document them minimally
750 :
751 :			* tests/simple.R: add a few examples for these
752 :
753 :	maechler	1696	2006-12-11 Martin Maechler <maechler@stat.math.ethz.ch>
754 :
755 :			* R/Tsparse.R ([): fix long standing typo in symmetric case
756 :			* man/dsCMatrix-class.Rd: add example exhibiting the above case
757 :
758 :	bates	1691	2006-12-10 Douglas Bates <bates@stat.wisc.edu>
759 :
760 :			* src/CHMfactor.c (CHMfactor_to_sparse): change LDL factorization
761 :			to LL before converting to a sparse matrix. (The LDL form can be
762 :			converted to a sparse matrix but it is implicitly a unit
763 :			triangular matrix and a diagonal matrix overwritten on the diagonal.)
764 :
765 :			2006-12-09 Douglas Bates <bates@stat.wisc.edu>
766 :
767 :			* src/chm_common.c (chm_factor_to_SEXP): allocate and fill the Dim slot.
768 :
769 :	bates	1688	2006-12-08 Douglas Bates <bates@stat.wisc.edu>
770 :
771 :			* DESCRIPTION (Version): updated -> release 0.9975-7
772 :			* src/{init.c,chm_common.c}, inst/include/*: export cholmod_analyze_p
773 :
774 :	maechler	1682	2006-11-30 Martin Maechler <maechler@stat.math.ethz.ch>
775 :
776 :			* R/diagMatrix.R (%*%): write a direct [diag o Csparse] method
777 :
778 :	bates	1681	2006-11-29 Douglas Bates <bates@stat.wisc.edu>
779 :
780 :			* src/dgeMatrix.c (dgeMatrix_solve): Check error code from dgetri.
781 :			* tests/dg_Matrix.R: Add Barry Rowlingson's test of a matrix that
782 :			is exactly singular.
783 :
784 :	maechler	1674	2006-11-07 Martin Maechler <maechler@stat.math.ethz.ch>
785 :
786 :			* DESCRIPTION (Date): updated -> release 0.9975-6
787 :
788 :	maechler	1673	2006-11-06 Martin Maechler <maechler@stat.math.ethz.ch>
789 :
790 :			* R/Csparse.R (replCmat): symmetric indexing of symmetric matrix
791 :			now returns symmetric.
792 :
793 :			* R/zzz.R ("diag<-"): replace "diag<-" in base for R <= 2.4.x
794 :
795 :			* R/Matrix.R (.M.sub.i.2col): new, for M[ cbind(i,j) ] indexing.
796 :			* R/Matrix.R (.M.repl.i.2col): new, for M[ cbind(i,j) ] <- value
797 :
798 :			* R/Auxiliaries.R (.type.kind): added
799 :
800 :			2006-11-04 Martin Maechler <maechler@stat.math.ethz.ch>
801 :
802 :			* src/cs.[ch]: updated to CSparse Version 2.0.3 by simply
803 :			running src/CSparse_install.sh
804 :
805 :			* R/denseMatrix.R: "[": keep symmetric on symmetric indexing.
806 :
807 :	maechler	1665	2006-11-03 Martin Maechler <maechler@stat.math.ethz.ch>
808 :
809 :			* src/dsCMatrix.c (dsCMatrix_Csparse_solve): new
810 :			* R/dsCMatrix.R (solve): "fully-sparse" using the above.
811 :
812 :			* R/AllClass.R: "pMatrix" now also inherits from "generalMatrix"
813 :
814 :			* tests/Class+Meth.R (tstMatrixClass): now assure
815 :			the (important in method programming) property :
816 :
817 :			###>> Every "Matrix" is either
818 :			###>> "general*", "symmetric*", "triangular*" or "diagonal*"
819 :
820 :			(where "*" stands for "Matrix")
821 :
822 :			* R/Auxiliaries.R (diagU2N): now .Call()s Csparse_diagU2N for <Csparse>
823 :
824 :			* R/dMatrix.R (Compare(<dMatrix>,<dMatrix>): update and
825 :			* tests/validObj.R: checks for "comparison"
826 :
827 :			* R/sparseMatrix.R ([): improved indexing for sparse;
828 :			trying to keep <symmetric>[ n, n] symmmetric
829 :
830 :			* tests/indexing.R: indexing for logical sparse now ok
831 :
832 :
833 :	maechler	1660	2006-11-02 Martin Maechler <maechler@stat.math.ethz.ch>
834 :
835 :	maechler	1661	* src/Tsparse.c: use xTsparse_validate() , and hence remove
836 :
837 :			* src/{ltC,lsC,lgT}Matrix.[ch]: removed
838 :
839 :			2006-11-02 Martin Maechler <maechler@stat.math.ethz.ch>
840 :
841 :	maechler	1660	* R/AllClass.R (Matrix-class): check length of dimnames in validity.
842 :
843 :			* tests/simple.R: validObject() checking the above.
844 :
845 :	maechler	1665	* src/dgCMatrix.c (xCMatrix_validate): new, small and simple,
846 :	maechler	1660	replacing both dgCMatrix_validate and lgCM*.
847 :
848 :			* src/Csparse.c (Csparse_dense_prod, etc): do not lose dimnames;
849 :			fix dimnames setting in other places.
850 :			* src/chm_common.c (chm_dense_to_SEXP): now can pass dimnames
851 :
852 :	maechler	1659	2006-11-01 Martin Maechler <maechler@stat.math.ethz.ch>
853 :
854 :	maechler	1660	* R/Csparse.R,src/Csparse.c, etc: tcrossprod(<CsparseM>,<CsparseM>)
855 :
856 :			* R/sparseMatrix.R (isSymmetric): drop 'factors' slot for
857 :			symmetry test, via
858 :	maechler	1659	* R/Auxiliaries.R (.as.dgC.0.factors):
859 :
860 :	bates	1657	2006-11-01 Douglas Bates <bates@r-project.org>
861 :
862 :			* R/Csparse.R,src/Csparse.c,tests/matprod.R,
863 :			man/CsparseMatrix-class.Rd: crossprod(<CsparseMatrix>,
864 :			<CsparseMatrix>) added
865 :
866 :	maechler	1655	2006-10-30 Martin Maechler <maechler@stat.math.ethz.ch>
867 :
868 :			* tests/matprod.R: add a variation of Harri's example
869 :
870 :			* R/dsparseMatrix.R: fix crossprod(<dsparse>, <dge>) to *not*
871 :			recursive infinitely.
872 :
873 :			* R/dgCMatrix.R: + solve(<sparse>, <sparse>)
874 :
875 :			* tests/indexing.R: add test for the "<" bug fixed 10-27 in R/dMatrix.R
876 :
877 :			2006-10-28 Martin Maechler <maechler@stat.math.ethz.ch>
878 :
879 :			* tests/Class+Meth.R (tstMatrixClass): more: use non-trivial
880 :			matrix if possible; test m+m == 2*m; now test dgRMatrix.
881 :			* R/dgRMatrix.R (.to.dgR): a few more coercions, in order to
882 :			satisfy the above test.
883 :
884 :	maechler	1654	2006-10-27 Martin Maechler <maechler@stat.math.ethz.ch>
885 :
886 :	maechler	1655	* R/Matrix.R (Ops): <Matrix> o <matrix> method added
887 :
888 :	maechler	1654	* R/dgCMatrix.R: solve(a, b="missing") based on
889 :			* src/dgCMatrix.c (dgCMatrix_matrix_solve): extend to work with
890 :			RHS = NULL.
891 :
892 :			* R/diagMatrix.R (diagdiagprod): extend %*% etc to ldiMatrix;
893 :			add more (needed) [t]crossprod() methods.
894 :
895 :			* man/ddiMatrix-class.Rd: more info, notably on 'diag'
896 :
897 :			* R/Auxiliaries.R (as_CspClass): cleanup
898 :			(drop0): internal utility for "Csparse_drop(*, 0)"
899 :			(.bail.out.2): encourage active feedback
900 :
901 :			2006-10-26 Martin Maechler <maechler@stat.math.ethz.ch>
902 :
903 :			* R/dMatrix.R(Compare): new(), then slots [no validity check]
904 :
905 :			* src/Csparse.c (Csparse_validate): fixed (and more efficient in
906 :			non-valid or 'sorted' case).
907 :
908 :			* R/dsparseMatrix.R: add "chol" method.
909 :			* R/ddenseMatrix.R: ditto
910 :
911 :			* R/diagMatrix.R (Ops): group methods for <diagonal> o <sparse>
912 :			* NAMESPACE (Ops)
913 :			* R/diagMatrix.R (diag2T): simple utility used "higher level"
914 :			coercion; deprecating direct lower level coercions.
915 :
916 :			* R/*.R (seq): use seq_len() and seq_along() where possible.
917 :
918 :
919 :	maechler	1647	2006-10-23 Martin Maechler <maechler@stat.math.ethz.ch>
920 :
921 :			* DESCRIPTION (Version): 0.9975-5 ready for release
922 :
923 :	bates	1646	2006-10-20 Douglas Bates <bates@stat.wisc.edu>
924 :
925 :			* src/init.c (R_init_Matrix): export more cholmod CCallable functions.
926 :
927 :	maechler	1642	2006-10-20 Martin Maechler <maechler@stat.math.ethz.ch>
928 :
929 :			* R/AllClass.R (corMatrix): add 'validity' check;
930 :			comment out unused "LDL" class definition
931 :			* NAMESPACE: mention, but do not export "LDL" class
932 :			* R/corMatrix.R: new (simple), needed for R-devel with
933 :			* tests/Class+Meth.R (tstMatrixClass): 1 exception for corMatrix
934 :			coerce and t() exceptions for all 5 'Mat.MatFact' classes.
935 :
936 :	bates	1641	2006-10-19 Douglas Bates <bates@stat.wisc.edu>
937 :
938 :			* src/chm_common.h: Add R_cholmod_start to initialize cholmod to
939 :			use Rprintf and R's error handling.
940 :
941 :	maechler	1635	2006-10-17 Martin Maechler <maechler@stat.math.ethz.ch>
942 :
943 :			* R/diagMatrix.R (%*%): rep(*, each = .) in Matrix %*% diagonal.
944 :			* tests/matprod.R: add tests for the bug fixed.
945 :
946 :	bates	1624	2006-10-11 Douglas Bates <bates@stat.wisc.edu>
947 :
948 :			* src/HBMM.[ch]: remove HarwellBoeing format for writing.
949 :			* src/SOURCES_C.mkf (SOURCES_C): no longer compile iohb.c
950 :
951 :			2006-10-06 Douglas Bates <bates@stat.wisc.edu>
952 :
953 :	bates	1629	* R/d[gs]CMatrix.R: deprecate the writeHB function. Use writeMM instead.
954 :	bates	1624
955 :	maechler	1618	2006-10-06 Martin Maechler <maechler@stat.math.ethz.ch>
956 :
957 :			* DESCRIPTION (Version): 0.9975-3
958 :
959 :			* R/diagMatrix.R (bdiag): new function constructing block diagonal
960 :			(sparse) matrices.
961 :			* man/bdiag.Rd: docu + examples
962 :
963 :	maechler	1619	* R/Csparse.R (replCmat): calling new Csparse_drop() now.
964 :
965 :	maechler	1618	* src/Csparse.c (Csparse_general_to_symmetric, Csparse_drop): new functions
966 :			* R/lsCMatrix.R: three more coercions to lsC (thanks to the above)
967 :
968 :			* R/diagMatrix.R (Diagonal): '[<-' method for diag.matrices such
969 :			that result is sparse or diagonal (and not dense).
970 :
971 :			* man/Subassign-methods.Rd: fix examples
972 :
973 :			* R/Matrix.R (Matrix): Matrix(0, *) or Matrix(*, sparse=TRUE)
974 :			should always return a sparse (and not sometimes a diagonal) matrix.
975 :
976 :	maechler	1615	2006-10-05 Martin Maechler <maechler@stat.math.ethz.ch>
977 :
978 :			* R/Matrix.R ([<-): also for value "Matrix" or "matrix"
979 :
980 :	bates	1613	2006-10-04 Douglas Bates <bates@stat.wisc.edu>
981 :
982 :			* DESCRIPTION (Version): 0.9975-2
983 :	maechler	1615
984 :	bates	1613	* inst/include/Matrix_stubs.c (M_cholmod_sparse_to_triplet): export more symbols
985 :
986 :	bates	1611	2006-10-02 Douglas Bates <bates@R-project.org>
987 :
988 :			* tests/dg_Matrix.R: Simplify test taking into account new code.
989 :
990 :	maechler	1599	2006-09-29 Martin Maechler <maechler@stat.math.ethz.ch>
991 :
992 :	maechler	1600	* R/Csparse.R (replCmat): improve for missing i / j in non-simple cases
993 :
994 :	maechler	1599	* R/lsTMatrix.R: new files w/ missing methods
995 :			* R/nsTMatrix.R: " 'for completeness'
996 :
997 :			* tests/Class+Meth.R: a bit less 'not.ok.classes'
998 :
999 :			* R/Tsparse.R (t): generalized "t" method from "dgT*" to "Tsparse*"
1000 :
1001 :
1002 :	bates	1595	2006-09-28 Douglas Bates <bates@R-project.org>
1003 :
1004 :			* src/dppMatrix.h: Ensure definition of dspMatrix_validate is
1005 :			included.
1006 :
1007 :			* src/init.c, inst/include/{Matrix.h,Matrix_stubs.h,cholmod.h}:
1008 :			Export C-callable functions used in Zt_create in lme4.
1009 :
1010 :	maechler	1592	2006-09-28 Martin Maechler <maechler@stat.math.ethz.ch>
1011 :
1012 :			* DESCRIPTION (Version): 0.9975-1
1013 :
1014 :			* tests/simple.R: less checks fail; using NA, found that our
1015 :			kronecker() is not base-compatible with NA's.
1016 :
1017 :			* R/dMatrix.R: "Compare" method now implemented for all cases
1018 :
1019 :			* R/Auxiliaries.R (indTri): == which([lower/upper].tri( * )) new utility
1020 :
1021 :			* man/dtpMatrix-class.Rd: mention length of 'x' slot
1022 :
1023 :			* src/dtpMatrix.c (dtpMatrix_validate): fix check
1024 :			* src/dspMatrix.c (dspMatrix_validate): ditto
1025 :
1026 :			* R/dtTMatrix.R (gt2tT): fix ("l" -> "n")
1027 :			including coercion to [nl]tTMatrix.
1028 :
1029 :			* R/diagMatrix.R (show): print a header line as for other classes.
1030 :
1031 :			2006-09-27 Martin Maechler <maechler@stat.math.ethz.ch>
1032 :
1033 :			* src/Makefile.win (SUBDIRS): fix typo
1034 :
1035 :	maechler	1583	2006-09-19 Martin Maechler <maechler@stat.math.ethz.ch>
1036 :
1037 :			* DESCRIPTION (Date): ready to release 0.9975-0 to CRAN
1038 :
1039 :	bates	1577	2006-09-18 Douglas Bates <bates@stat.wisc.edu>
1040 :
1041 :			* R/[CT]sparse.R (crossprod and tcrossprod): Handle the cases for x
1042 :			symmetric and y missing in R code using %*% (cholmod_aat doesn't
1043 :			accept a symmetric matrix).
1044 :			* tests/group-methods.R: Uncomment test of crossprod applied to
1045 :			lsCMatrix objects.
1046 :
1047 :	maechler	1575	2006-09-18 Martin Maechler <maechler@stat.math.ethz.ch>
1048 :
1049 :			* R/AllClass.R (symmetricMatrix): add validity method (available
1050 :			in C for a long time). Many "n..Matrix": drop (wrong) validity arg.
1051 :
1052 :			* src/lgCMatrix.c (lgCMatrix_validate): check 'x' slot (!)
1053 :
1054 :			* tests/indexing.Rout.save:
1055 :			* tests/indexing.R: additions, mainly for 'lsparse'
1056 :
1057 :			* R/diagMatrix.R (Diagonal) & coercion to lgTMatrix: fixes for NA
1058 :			case.
1059 :
1060 :			* R/Auxiliaries.R (nz.NA): new utility now used in nnzero()
1061 :
1062 :	maechler	1571	2006-09-16 Martin Maechler <maechler@stat.math.ethz.ch>
1063 :
1064 :	maechler	1572	* R/sparseMatrix.R (prSpMatrix): print logical NAs "visibly"
1065 :			as 'N' (1-letter - Ok?)
1066 :
1067 :	maechler	1571	* tests/group-methods.R: add test for logical + NAs
1068 :
1069 :			* R/dMatrix.R ("Compare"): fix to work with NA's
1070 :
1071 :			* R/AllClass.R: "Cholesky" etc now inherit from MatrixFactorization.
1072 :
1073 :			* src/lgCMatrix.c (ncsc_to_matrix): renamed from lcsc_to_matrix()
1074 :			which is implemented.
1075 :
1076 :	maechler	1565	2006-09-15 Martin Maechler <maechler@stat.math.ethz.ch>
1077 :
1078 :	maechler	1571	* src/chm_common.c: coerce logical <-> double instead of
1079 :			typecasting; needed for "l" matrix handling in cholmod.
1080 :	maechler	1565
1081 :	maechler	1571	* tests/other-pkgs.R (graph): small extension in "graph" checks.
1082 :
1083 :	maechler	1565	* R/sparseMatrix.R (graphNEL -> Tsparse): method for weight case.
1084 :			(Tsp2grNEL): other fixes needed
1085 :
1086 :	maechler	1548	2006-09-11 Martin Maechler <maechler@stat.math.ethz.ch>
1087 :
1088 :			* R/AllClass.R ("nMatrix"): and subclasses for "nonzero pattern"
1089 :			Matrices, since "lMatrix", also "lsparseM" can have NA
1090 :			* R/ndenseMatrix.R, etc: new source files
1091 :			* man/nsparseMatrix-classes.Rd, etc: new help files
1092 :			* tests/: adaptions
1093 :			* src/chm_common.c (chm_dense_to_SEXP): and others:
1094 :			new 'Rkind' argument: "l*" and "d*" both use CHOLMOD_REAL
1095 :	maechler	1582	* src/Csparse.c, etc: ditto
1096 :	maechler	1548
1097 :	bates	1546	2006-09-11 Douglas Bates <bates@R-project.org>
1098 :
1099 :			* src/Mutils.[ch],init.c inst/include/*.h: Move the
1100 :			alloc_d**Matrix functions to the lme4 package.
1101 :
1102 :	bates	1543	2006-09-09 Douglas Bates <bates@R-project.org>
1103 :
1104 :			* src/dsCMatrix.c (dsCMatrix_Cholesky): igoring LDL = FALSE now
1105 :	maechler	1544	fixed
1106 :	bates	1543
1107 :	maechler	1544	2006-09-09 Martin Maechler <maechler@stat.math.ethz.ch>
1108 :
1109 :	maechler	1548	* R/lMatrix.R: new
1110 :
1111 :	maechler	1544	* R/sparseMatrix.R (Tsp2grNEL): do not yet use graph::foo()
1112 :
1113 :			* R/dgeMatrix.R: do not define tcrossprod() methods for "matrix"
1114 :	maechler	1582	* man/tcrossprod.Rd: ditto
1115 :	maechler	1544
1116 :	bates	1538	2006-09-08 Douglas Bates <bates@stat.wisc.edu>
1117 :
1118 :			* inst/include/Matrix_stubs.c,Matrix.h: Add declarations and stubs
1119 :			for exported functions
1120 :			* src/Makefile, src/CHOLMOD/Lib/Makefile, src/Metis,CAMD,CCOLAMD:
1121 :			Remove partitioning algorithms for sparse matrix reordering. The
1122 :			copyright on the Metis code was problematic and the methods were
1123 :			rarely used.
1124 :			* src/triplet_to_col.[ch],MMHB.[ch]: Remove triplet_to_col. Such
1125 :			operations are now done entirely in CHOLMOD code.
1126 :
1127 :	bates	1517	2006-09-06 Douglas Bates <bates@R-project.org>
1128 :
1129 :			* src/Mutils.h: Remove functions that are no longer used.
1130 :
1131 :	bates	1507	2006-09-04 Douglas Bates <bates@R-project.org>
1132 :
1133 :			* src/dtCMatrix.c (dtCMatrix_validate): rename functions.
1134 :			* src/DEPS.mkf: update
1135 :
1136 :	maechler	1481	2006-09-02 Martin Maechler <maechler@stat.math.ethz.ch>
1137 :
1138 :			* created branches/Matrix-for-R-2.3.x; on trunk: do
1139 :			* DESCRIPTION (Version): 0.9975-0
1140 :			(Depends): R (>= 2.4.0)
1141 :
1142 :	bates	1475	2006-09-01 Douglas Bates <bates@R-project.org>
1143 :
1144 :			* R/sparseMatrix.R: Added direct method to CsparseMatrix from graphNEL
1145 :
1146 :	maechler	1472	2006-09-01 Martin Maechler <maechler@stat.math.ethz.ch>
1147 :
1148 :			* R/sparseMatrix.R: add coercion from "ANY" to "sparseMatrix"
1149 :			* R/denseMatrix.R: add coercion from "ANY" to "denseMatrix"
1150 :
1151 :			* R/Matrix.R ([): use nargs() to disambiguate M[i] and M[i,]
1152 :
1153 :			2006-08-31 Martin Maechler <maechler@stat.math.ethz.ch>
1154 :
1155 :			* R/sparseMatrix.R (Arith): moved Arith group method one-level up
1156 :			from "dsparse" to "sparse" and now go via "Csparse" instead of "dgC"
1157 :	maechler	1582	* R/dsparseMatrix.R: ditto
1158 :			* R/Csparse.R: ditto
1159 :	maechler	1472
1160 :			2006-08-31 Martin Maechler <maechler@stat.math.ethz.ch>
1161 :
1162 :			* R/dMatrix.R (Compare): improve availability of "<", etc
1163 :			* R/Auxiliaries.R (asTuniq): new; also make use of R 2.4.x print(*,max)
1164 :
1165 :	maechler	1467	2006-08-30 Martin Maechler <maechler@stat.math.ethz.ch>
1166 :
1167 :			* R/dgCMatrix.R: aargh: "Arith(<dgC>, numeric)" was wrong because
1168 :			of a 0-index which was used as 1-index (..hmm)
1169 :
1170 :			* R/sparseMatrix.R (prSpMatrix): fix printing an all-0 sparse Matrix
1171 :
1172 :			* R/Auxiliaries.R (all0, is0): for 0-testing in presence of NA's
1173 :			* R/Auxiliaries.R (isTriMat): use all0() for 0-testing.
1174 :	maechler	1582	(.is.diagonal): ditto
1175 :	maechler	1467
1176 :			* R/lgTMatrix.R: as("matrix", "lgTMatrix"): warn about NA's
1177 :
1178 :			* R/Matrix.R (Matrix): also work for NA data
1179 :
1180 :	maechler	1455	2006-08-28 Martin Maechler <maechler@stat.math.ethz.ch>
1181 :
1182 :			* R/Matrix.R (Matrix): + 'forceCheck' argument; dimnames setting
1183 :			in all cases.
1184 :
1185 :	bates	1453	2006-08-27 Douglas Bates <bates@R-project.org>
1186 :
1187 :			* src/dense.[ch],init.c, R/ddenseMatrix.R, man/band.Rd
1188 :			(ddense_band): Added triu, tril and band for ddenseMatrix objects.
1189 :
1190 :	maechler	1447	2006-08-25 Martin Maechler <maechler@stat.math.ethz.ch>
1191 :
1192 :			* src/Mutils.c (dup_mMatrix_as_dgeMatrix): added all subclasses of
1193 :			subclasses of "ddenseMatrix"
1194 :			* src/init.c et al: outcomment dtrM*_as_dge* and dsyM*_as_dge*_
1195 :			* R/ddenseMatrix.R et al: setAs("ddenseMatrix", "dgeMatrix", ..)
1196 :			instead of half dozen specialized ones.
1197 :
1198 :	bates	1445	2006-08-25 Douglas Bates <bates@R-project.org>
1199 :
1200 :			* R/lmer.R (qqmath method): Bug fix provided by Emmanuel Tillard
1201 :			<tillard@cirad.fr> - ordering standard errors to match effects.
1202 :
1203 :	bates	1439	2006-08-24 Douglas Bates <bates@R-project.org>
1204 :	bates	1431
1205 :	bates	1439	* src/lsCMatrix.c (lsCMatrix_trans): Remove lsCMatrix_chol based
1206 :			on R_ldl.
1207 :			* R/lCholCMatrix.R,
1208 :			src/[dl]CholCMatrix.[ch],R_ldl.[ch],Metis_utils.[ch]: removed
1209 :			* src/dsCMatrix.c (dsCMatrix_to_dgTMatrix): use CHOLMOD
1210 :			* many files in ./R and ./src: Use more general version of
1211 :			dup_mMatrix_as_dgeMatrix to simplify method definitions.
1212 :	bates	1442	* src/Mutils.c (dup_mMatrix_as_dgeMatrix): Add ddiMatrix,
1213 :			dtpMatrix, dspMatrix and dppMatrix conversions.
1214 :
1215 :	maechler	1447
1216 :	bates	1439	2006-08-23 Douglas Bates <bates@R-project.org>
1217 :
1218 :			* R/AllClass.R,lCholCMatrix.R,src/SOURCES_C.mkf,init.c,NAMESPACE:
1219 :			Remove classes lCholCMatrix and dCholCMatrix based on R_ldl code.
1220 :	bates	1431	* src/dgeMatrix.c: Ensure 'factors' slot exists in result of
1221 :			dgeMatrix_crossprod (may need to do this in other places).
1222 :			* R/AllGeneric.R,dsCMatrix.R, src/dscMatrix.[ch]: Add Cholesky
1223 :			generic and method for dsCMatrix. Use CHOLMOD for chol().
1224 :
1225 :	bates	1414	2006-08-22 Douglas Bates <bates@R-project.org>
1226 :
1227 :			* src/Mutils.c (dup_mMatrix_as_dgeMatrix): updated for general
1228 :			types of classed Matrices, matrices or numeric or logical vectors.
1229 :	bates	1423	* src/init.c: register dup_mMatrix_as_dgeMatrix for coercions.
1230 :			* src/chm_common.c,Mutils.h (as_cholmod_factor): Move check_class
1231 :			to Mutils.h (as an inline) and change name to Matrix_check_class;
1232 :			fixes in as_cholmod_factor and chm_factor_to_SEXP.
1233 :			* src/dsCMatrix.[ch]: Use CHOLMOD for dsCMatrix_chol and
1234 :			dsCMatrix_matrix_solve. Comment out vestigial functions.
1235 :			* src/Csparse.c: use diag_P and uplo_P macros.
1236 :	maechler	1447
1237 :	bates	1405	2006-08-21 Douglas Bates <bates@R-project.org>
1238 :
1239 :			* src/lmer.c (internal_mer_RZXinv): Fix memory leak caught by
1240 :	maechler	1447	valgrind.
1241 :	bates	1411	* tests/matprod.R: Add tests to verify that 'solve' and '%*%' are
1242 :			inverses.
1243 :			* src/sparseQR.c (sparseQR_validate): add new validation test, fix
1244 :			-Wall warnings.
1245 :			* src/dppMatrix.c,dtrMatrix.c,dgCMatrix.c,dgeMatrix.c,dspMatrix.c:
1246 :			Use dup_mMatrix_as_dgeMatrix.
1247 :	maechler	1447
1248 :	bates	1403	2006-08-20 Douglas Bates <bates@R-project.org>
1249 :
1250 :			* src/sparseQR.c: Fix thinko in sparseQR_resid_fitted.
1251 :			* tests/sparseQR.R: Added
1252 :			* man/sparseQR-class.Rd: Document methods for qr.* generics
1253 :			* R/sparseQR.R: Return correct # of coefs; fix cut-and-paste errors
1254 :
1255 :	bates	1398	2006-08-19 Douglas Bates <bates@R-project.org>
1256 :
1257 :			* NAMESPACE, R/sparseQR.R, src/init.c,sparseQR.[ch],SOURCES_C.mkf:
1258 :			Added methods for sparseQR for qr.qy, qr.qty, qr.coef, qr.resid
1259 :			and qr.fitted.
1260 :			* src/Mutils.[ch]: Added dup_mMatrix_as_dgeMatrix utility
1261 :			* src/dgCMatrix.c: Check for ordering before storing q in dgCMatrix_QR
1262 :
1263 :	maechler	1389	2006-08-18 Martin Maechler <maechler@stat.math.ethz.ch>
1264 :
1265 :			* R/AllGeneric.R: add "qr" and "chol" generics; via 'trick' since
1266 :			the base version has no "..." argument.
1267 :
1268 :			* R/sparseMatrix.R (prSpMatrix): fix the triangular unit diagonal case.
1269 :
1270 :			* R/Matrix.R: define and
1271 :			* NAMESPACE: export as.numeric() and as.logical() methods.
1272 :			Let's hope these do not badly slow down something...
1273 :			Finally export the zapsmall() method.
1274 :
1275 :	bates	1388	2006-08-17 Douglas Bates <bates@R-project.org>
1276 :
1277 :			* src/dgCMatrix.[ch] (dgCMatrix_matrix_solve), src/init.c,
1278 :			R/dgCMatrix.R: solve methods for dgCMatrix and dense RHS.
1279 :			* src/dtCMatrix.c :Remove code that is no longer used
1280 :			* R/dtCMatrix.R: Use C code for diagU2N in CsparseMatrix classes
1281 :
1282 :	bates	1370	2006-08-14 Douglas Bates <bates@R-project.org>
1283 :
1284 :	bates	1373	* src/Csparse.[ch],init.c (Csparse_to_logical): Added utilities
1285 :			Csparse_to_logical and Csparse_symmetric_to_general.
1286 :			* R/dgCMatrix.R,dsCMatrix.R,Csparse.R : Consolidate general
1287 :	maechler	1389	coercion methods between CsparseMatrix and TsparseMatrix.
1288 :	bates	1373
1289 :			2006-08-14 Douglas Bates <bates@R-project.org>
1290 :
1291 :	bates	1370	* R/dtCMatrix.R,dgCMatrix.R,Csparse.R src/init.c,dgCMatrix.[ch],
1292 :			Csparse.[ch],chm_common.c,dense.c : Use CHOLMOD code and methods
1293 :			for CsparseMatrix, TsparseMatrix, denseMatrix or matrix when
1294 :			possible.
1295 :
1296 :	bates	1368	2006-08-12 Douglas Bates <bates@R-project.org>
1297 :
1298 :			* src/chm_common.[ch],Csparse.[ch],Tsparse.[ch],CHMfactor.c,dtTMatrix.c,
1299 :			dgTMatrix.c,dgCMatrix.c,dsCMatrix.c,dtTMatrix.c, R/dsTMatrix.R,
1300 :			Tsparse.R,Csparse.R,dgTMatrix.R,dsCMatrix.R,lsCMatrix.R:
1301 :			generalize conversions between TsparseMatrix, CsparseMatrix,
1302 :			denseMatrix and matrix. Preserve triangularity property and
1303 :			propagate Dimnames in the easy cases.
1304 :
1305 :	bates	1365	2006-08-10 Douglas Bates <bates@R-project.org>
1306 :
1307 :			* src/lmer.c: adjust checks in glmer_init for S4SXP
1308 :			* tests/validObj.R: check of all(eq) should be all(eq@x) - worked
1309 :			before S4SXP but for the wrong reasons.
1310 :
1311 :	bates	1354	2006-08-08 Douglas Bates <bates@R-project.org>
1312 :
1313 :	bates	1360	* src/Csparse.c (Csparse_crossprod): tcrossprod result has stype = -1.
1314 :			Later modified to return the upper triangle only.
1315 :			* R/dgTMatrix.R: Remove vestigial crossprod and tcrossprod methods.
1316 :	maechler	1389
1317 :	bates	1352	2006-08-07 Douglas Bates <bates@R-project.org>
1318 :
1319 :			* src/Csparse.c (Csparse_crossprod): Set stype on result to avoid
1320 :			R-level conversion to a sparse symmetric class.
1321 :			* R/Tsparse.R,R/Csparse.R (crossprod and tcrossprod methods):
1322 :			Remove conversion to sparse symmetric classes (now done in C code).
1323 :
1324 :	maechler	1349	2006-08-07 Martin Maechler <maechler@stat.math.ethz.ch>
1325 :
1326 :	maechler	1351	* R/dgCMatrix.R: disable old crossprod and tcrossprod methods
1327 :			* man/band.Rd: adapt the \dontshow{} unit test.
1328 :
1329 :			2006-08-07 Martin Maechler <maechler@stat.math.ethz.ch>
1330 :
1331 :	maechler	1349	* DESCRIPTION (Version): 0.995-14 for CRAN
1332 :
1333 :			* tests/other-pkgs.R: oops: library(Matrix) outside *if* !
1334 :
1335 :			* R/sparseMatrix.R (Tsp2grNEL): fixed Tsparse -> graph coercion
1336 :			* tests/other-pkgs.R: more checks, sparseMatrix -> graph
1337 :
1338 :			* R/Auxiliaries.R (as_Tsparse, as_Rsparse): new
1339 :			* R/Tsparse.R (tril, triu, band): methods
1340 :	bates	1352	* R/dgRMatrix.R (tril, ...): ditto
1341 :			* man/band.Rd: ditto
1342 :	maechler	1349
1343 :			2006-08-04 Martin Maechler <maechler@stat.math.ethz.ch>
1344 :
1345 :			* R/Matrix.R (head, tail): directly use utils:::head.matrix
1346 :			to be up-to-date automatically.
1347 :
1348 :	maechler	1346	2006-08-03 Martin Maechler <maechler@stat.math.ethz.ch>
1349 :
1350 :			* DESCRIPTION (Version): 0.995-13 to be released to CRAN
1351 :
1352 :			* DESCRIPTION (Lazydata): no, instead of 'yes' because it fails for:
1353 :			* data/CAex.R, inst/external/CAex_slots.rda: replacing data/CAex.rda
1354 :			* data/KNex.R, inst/external/KNex_slots.rda: replacing data/KNex.rda
1355 :			such that the S4 objects are always created by the current version
1356 :			of R and 'Matrix' class definitions.
1357 :
1358 :	bates	1342	2006-08-01 Douglas Bates <bates@R-project.org>
1359 :
1360 :			* R/lmer.R (LMEoptimize method), tests/lmer.R,
1361 :	maechler	1346	inst/external/test3comp.rda: Added warnings for convergence on
1362 :	bates	1342	boundary and test cases.
1363 :
1364 :			* src/lmer.c (mer_postVar): Modified to return the variances that
1365 :			are marginal to the fixed effects, not conditional on them (which
1366 :			is what the bVar slot contents represent).
1367 :
1368 :	bates	1338	2006-07-31 Douglas Bates <bates@R-project.org>
1369 :
1370 :			* NAMESPACE, src/lmer.c, R/lmer.R (hatTrace): Add the hatTrace
1371 :			function which calls the C function mer_hat_trace2.
1372 :	maechler	1346
1373 :	bates	1342	* man/ranef.Rd: Include description of "postVar" argument and
1374 :			producing a caterpillar plot.
1375 :	bates	1338
1376 :	maechler	1335	2006-07-31 Martin Maechler <maechler@stat.math.ethz.ch>
1377 :
1378 :			* NAMESPACE: change "correlation" to "corMatrix"
1379 :			* R/AllClass.R: to avoid clash with S3 class in 'nlme'.
1380 :	bates	1352	* R/dpoMatrix.R: ditto
1381 :			* R/lmer.R: ditto
1382 :	maechler	1335
1383 :	bates	1338	2006-07-28 Douglas Bates <bates@R-project.org>
1384 :
1385 :			* src/lmer.c (internal_mer_RZXinv): Split the calculation of the
1386 :			RZXinv slot's contents into a separate internal function that can
1387 :			be used in mer_hat_trace.
1388 :
1389 :	maechler	1331	2006-07-22 Martin Maechler <maechler@stat.math.ethz.ch>
1390 :
1391 :			* R/Matrix.R: Coercions "Matrix" -> (sparse|dense)Matrix
1392 :			via new smart
1393 :			* R/Auxiliaries.R (as_Csparse, as_dense, .M.shapse): new
1394 :			utility functions.
1395 :
1396 :
1397 :	maechler	1330	2006-07-21 Martin Maechler <maechler@stat.math.ethz.ch>
1398 :
1399 :	maechler	1331	* R/Csparse.R (tril, triu, band): do return *triangular* classed
1400 :			matrices when appropriate; band() even symmetric ones.
1401 :			(replCmat): extend to potentially all "CsparseMatrix"
1402 :			* R/Tsparse.R (replTmat): extend to all "TsparseMatrix"; hence
1403 :			allow subassignment for special sparse matrices.
1404 :
1405 :			* R/Auxiliaries.R (as_geClass): factor out the .M.kind() functionality
1406 :
1407 :	maechler	1330	* src/lmer.c (mer_MCMCsamp, glmer_MCMCsamp): new 'verbose'
1408 :			argument; in glmer_*(): print only if(verbose).
1409 :
1410 :			speed-optimize a few places by moving REAL(.) out of loops.
1411 :
1412 :			* src/lmer.h, src/init.h, R/lmer.R: related to above.
1413 :
1414 :	maechler	1329	2006-07-20 Martin Maechler <maechler@stat.math.ethz.ch>
1415 :
1416 :			* R/Matrix.R("["): disable ("Matrix", i = "logical", j = "missing"),
1417 :			since that wrongly triggers also for M[ logi , ]
1418 :
1419 :			* R/denseMatrix.R: "[" methods now also work e.g. when indexing
1420 :			a symmetric matrix that results in a non-symmetric one.
1421 :			* R/Auxiliaries.R (as_geClass): new function used in "[" above.
1422 :
1423 :			* R/dMatrix.R: make round(M) work as round(M, 0)
1424 :
1425 :			* R/dgTMatrix.R (image): coordinate system and axis now use
1426 :			1-based indices, not 0-based ones.
1427 :
1428 :			* R/Tsparse.R (.ind.prep for "["): get rid of max(<empty>) warning.
1429 :			* tests/indexing.R: test it.
1430 :
1431 :			* NAMESPACE: export isSymmetric(); has been a generic in "base" for a while;
1432 :			* man/isSymmetric-methods.Rd: and document it.
1433 :
1434 :			* R/SparseM-conv.R: added coercion methods for some 'SparseM' matrices.
1435 :			* man/SparseM-conv.Rd: docu them
1436 :
1437 :			* tests/other-pkgs.R: renamed from tests/graph.R and add example
1438 :			for 'SparseM' conversions
1439 :
1440 :			2006-07-17 Douglas Bates <Douglas.Bates@R-project.org>
1441 :
1442 :			* R/Matrix.R (head): added head() and tail() methods.
1443 :
1444 :			2006-07-17 Martin Maechler <maechler@stat.math.ethz.ch>
1445 :
1446 :			* DESCRIPTION (Version): 0.995-12 released to CRAN
1447 :
1448 :	maechler	1319	2006-07-15 Martin Maechler <maechler@stat.math.ethz.ch>
1449 :
1450 :			* tests/simple.R: add check for correct dsT -> dgT coercion;
1451 :			add check for correct printing of symmetric sparse matrices.
1452 :
1453 :			* R/Auxiliaries.R (non0ind): return *all* non-0 entry indices also
1454 :			for sparse symmetric matrices.
1455 :
1456 :			* src/dsTMatrix.c (dsTMatrix_as_dgTMatrix): do not copy the
1457 :			diagonal twice.
1458 :
1459 :	bates	1316	2006-07-11 Douglas Bates <Douglas.Bates@R-project.org>
1460 :
1461 :			* src/dsTMatrix.c (dsTMatrix_as_dgTMatrix): Fix a case of INTEGER
1462 :	maechler	1319	being applied to the x slot (detected by Brian Ripley).
1463 :	bates	1316
1464 :	maechler	1315	2006-07-10 Martin Maechler <maechler@stat.math.ethz.ch>
1465 :
1466 :			* src/dgCMatrix.c (dgCMatrix_validate): 'p' slot must have correct length.
1467 :
1468 :			* R/Auxiliaries.R (isTriC): fix buglet (we were 1-based!)
1469 :
1470 :			2006-07-08 Martin Maechler <maechler@stat.math.ethz.ch>
1471 :
1472 :			* src/lgCMatrix.c (lgCMatrix_diag): new function
1473 :			* R/lgCMatrix.R (diag): for new method
1474 :
1475 :			* R/AllClass.R (TsparseMatrix): do use Tsparse_validate
1476 :			==> construction of illegal "*gTMatrix" via new() should
1477 :			now be much less easy:
1478 :			* tests/Class+Meth.R: assertError() for some illegal "dgT*"
1479 :
1480 :			* R/Matrix.R (Matrix): Matrix(0, nrow,ncol) now "goes sparse"
1481 :			directly.
1482 :			* man/Matrix.Rd: documents it.
1483 :
1484 :	bates	1311	2006-07-06 Douglas Bates <bates@R-project.org>
1485 :
1486 :			* src/pedigree.c (pedigree_inbreeding): Correction in
1487 :			initialization. This function is not currently being used and is
1488 :			not fully tested.
1489 :
1490 :	bates	1312	* NAMESPACE, R/{AllClass.R,lmer.R}, src/{init.c,lmer.c}:
1491 :			Introduced the glmer class. Added code for mcmcmsamp on glmer
1492 :			objects. Modified validity check on pedigree objects to account
1493 :			for nonparallel patterns of missingness of parents.
1494 :	bates	1311
1495 :	bates	1313	* man/{lmer-class.Rd,mcmcsamp.Rd}: Update documentation for glmer
1496 :			class.
1497 :	maechler	1315
1498 :			2006-07-01 Martin Maechler <maechler@stat.math.ethz.ch>
1499 :
1500 :			* R/pMatrix.R: coercion pMatrix -> Tsparse
1501 :
1502 :	bates	1300	2006-06-12 Douglas Bates <bates@R-project.org>
1503 :
1504 :	maechler	1319	* DESCRIPTION (Version): 0.995-11 released to CRAN
1505 :
1506 :	bates	1300	* R/lmer.R (mcmcsamp method): Corrected arrangments of names on
1507 :			the output from mcmcsamp.
1508 :
1509 :	bates	1298	2006-06-10 Douglas Bates <bates@R-project.org>
1510 :
1511 :	bates	1300	* R/lmer.R (simulestimate): added C code for calculating the trace
1512 :			of the hat matrix.
1513 :	bates	1298
1514 :	maechler	1295	2006-06-09 Martin Maechler <maechler@stat.math.ethz.ch>
1515 :
1516 :			* R/diagMatrix.R (setAs): define coercion methods to sparse matrix
1517 :			classes.
1518 :	maechler	1315	* R/sparseMatrix.R etc: multiplication of diagonal and sparse
1519 :	maechler	1295
1520 :	maechler	1290	2006-06-08 Martin Maechler <maechler@stat.math.ethz.ch>
1521 :
1522 :			* R/dgTMatrix.R (colSums): etc. All four of
1523 :			colSums(), rowSums(), colMeans(), rowMeans() now should work for
1524 :			all "Matrices".
1525 :
1526 :	bates	1288	2006-06-01 Douglas Bates <bates@stat.wisc.edu>
1527 :
1528 :			* R/lmer.R (panel.ci): Add a reference line at zero and a
1529 :			background grid to the qqmath plot of ranef.lmer.
1530 :
1531 :	bates	1287	2006-05-30 Douglas Bates <bates@stat.wisc.edu>
1532 :	bates	1284
1533 :	bates	1287	* R/lmer.R (expandSlash): Functions (non-exported) to allow nested
1534 :			grouping factors to be specified in the formula as (1|foo/bar).
1535 :
1536 :			2006-05-27 Douglas Bates <bates@stat.wisc.edu>
1537 :
1538 :	bates	1284	* R/lmer.R (findbars and others): Change check of is.numeric to
1539 :			!is.language to resolve the bug reported by Jacob Wegelin.
1540 :
1541 :			* src/pedigree.c (pedigree_inbreeding): Initial implementation of
1542 :			code to evaluate inbreeding coefficients without calculating T,
1543 :			based on code in Sargolzaei and Iwaisaki's paper.
1544 :
1545 :	bates	1283	2006-05-27 Douglas Bates <bates@stat.wisc.edu>
1546 :
1547 :			* R/{lmer.R,AllGeneric.R}, src/{init.c,lmer.[ch]}: Added local
1548 :			generic and mer methods for isNested and denomDF. This denomDF was
1549 :			an attempt to emulate that in lme but I don't think that makes
1550 :			sense. Use the trace of the hat matrix instead.
1551 :
1552 :	maechler	1271	2006-05-17 Martin Maechler <maechler@stat.math.ethz.ch>
1553 :
1554 :			* R/sparseMatrix.R: Matrix <-> graph methods: can no longer use
1555 :			the C code depending on a slot structure that's no longer valid.
1556 :	bates	1352	* src/dgTMatrix.c: ditto (also: src/init.c src/dgTMatrix.h)
1557 :	maechler	1271
1558 :
1559 :	bates	1268	2006-05-17 Douglas Bates <bates@stat.wisc.edu>
1560 :
1561 :			* R/{AllGeneric.R,Csparse.R},man/band.Rd,NAMESPACE: changed name
1562 :			of lowerTriMatrix generic and methods to tril (also upper to triu)
1563 :			and added a general band extractor.
1564 :
1565 :	bates	1267	2006-05-16 Douglas Bates <bates@stat.wisc.edu>
1566 :
1567 :			* R/pedigree.R (pedigree): Replace sire and dam values outside the
1568 :			allowable range with NAs. Added a corresponding check in the
1569 :			validity check for the pedigree class.
1570 :
1571 :			* R/[CT]sparse.R ([t]crossprod): The result of single-argument
1572 :			crossprod methods now inherits from symmetricMatrix.
1573 :
1574 :	bates	1265	2006-05-15 Douglas Bates <bates@stat.wisc.edu>
1575 :
1576 :			* R/AllGeneric.R (lowerTriMatrix): Added (but did not export)
1577 :			generics lowerTriMatrix and upperTriMatrix along with methods for
1578 :			the Csparse virtual class. Also added a C function Csparse_band
1579 :			that implements these methods by calling cholmod_band.
1580 :
1581 :	maechler	1264	2006-05-15 Martin Maechler <maechler@stat.math.ethz.ch>
1582 :
1583 :			* R/Tsparse.R ("["): column or row subsetting; @Dimnames[k] got
1584 :			erased when it was NULL. This led to invalid subselections!
1585 :
1586 :	bates	1259	2006-04-25 Douglas Bates <bates@stat.wisc.edu>
1587 :
1588 :			* R/dtCMatrix.R: avoid coercion of dtCMatrix object to dgCMatrix
1589 :			in method for "t" so as not to lose the unit diagonal property.
1590 :
1591 :	bates	1257	2006-04-19 Douglas Bates <bates@stat.wisc.edu>
1592 :
1593 :			* R/lmer.R, R/AllGeneric.R, NAMESPACE: Remove the postVar generic
1594 :			and methods. This is now an option to the ranef method for the
1595 :			mer class.
1596 :
1597 :			* src/cs_utils.c: Ensure that the nz component is -1 for a
1598 :			compressed column-oriented matrix. Minor formatting cleanup.
1599 :
1600 :			* man/lmer-class.Rd: Document the qqmath method for ranef.lmer
1601 :			objects.
1602 :
1603 :	maechler	1253	2006-04-19 Martin Maechler <maechler@stat.math.ethz.ch>
1604 :
1605 :			* R/Auxiliaries.R (diagU2N): new for the solve() methods in
1606 :			* R/dtCMatrix.R: where dgC -> dgT coercion now preserves diag = "U".
1607 :
1608 :	bates	1251	2006-04-15 Douglas Bates <bates@stat.wisc.edu>
1609 :
1610 :			* src/cs.[ch],src/cs_utils.[ch] : Added Tim Davis' CSparse library
1611 :			in cs.[ch] and utilities to interface to that code in cs_utils.[ch].
1612 :
1613 :			* R/dtCMatrix.R, src/dtCMatrix.[ch] : CSparse-based solve methods
1614 :			for the dtCMatrix class.
1615 :	maechler	1253
1616 :	bates	1247	2006-04-12 Douglas Bates <bates@stat.wisc.edu>
1617 :
1618 :			* R/pedigree.R, R/AllClass.R, NAMESPACE: added a pedigree class
1619 :			and methods for it.
1620 :
1621 :	maechler	1245	2006-04-12 Martin Maechler <maechler@stat.math.ethz.ch>
1622 :
1623 :			* R/dgCMatrix.R: add storage.mode(.) <- "double" for "matrix"
1624 :			arguments, such that M %*% 1:6 now works
1625 :			* Tests/matprod.R: test the above
1626 :
1627 :	bates	1244	2006-04-03 Douglas Bates <bates@stat.wisc.edu>
1628 :	bates	1243
1629 :			* R/lmer.R (qqmath,ranef.lmer-method): added a qqmath method for
1630 :			the ranef.lmer class.
1631 :
1632 :			* R/AllClass.R, NAMESPACE, R/lmer.R: Added a postVar generic and
1633 :			methods to extract the posterior variances from the bVar slot.
1634 :
1635 :	maechler	1238	2006-03-30 Martin Maechler <maechler@stat.math.ethz.ch>
1636 :
1637 :			* R/dtCMatrix.R: allow coercion from dgC* to triangular (dtC*)
1638 :			* R/dsCMatrix.R: and symmetric (dsC*) 'Csparse' matrices.
1639 :
1640 :			* R/Tsparse.R: Tsparse* -> Csparse* coercion now works and is tested in
1641 :			* tests/simple: (extended)
1642 :
1643 :			* R/sparseMatrix.R (isTriangular): now using much improved
1644 :			* R/Auxiliaries.R (isTriC): new triangularity check for *CMatrix
1645 :
1646 :	bates	1236	2006-03-23 Douglas Bates <bates@stat.wisc.edu>
1647 :
1648 :			* src/dsyMatrix.c (dsyMatrix_as_dspMatrix): Propagate DimNames
1649 :			(problem report from Franklin Parlamis). This should be done
1650 :	maechler	1238	generally.
1651 :	bates	1236
1652 :	bates	1234	2006-03-21 Douglas Bates <bates@stat.wisc.edu>
1653 :
1654 :			* R/AllClass.R,lmer.R: Change the name of the lmer.ranef class to
1655 :			ranef.lmer (like summary.lmer). Add the coef.lmer class and
1656 :			update the plot methods.
1657 :
1658 :	bates	1232	2006-03-20 Douglas Bates <bates@stat.wisc.edu>
1659 :
1660 :			* R/lmer.R (resid and ranef methods): Added methods for the
1661 :			"residuals" and "resid" generic but only for linear mixed model
1662 :			fits. Changed the ranef method to return a list of data frames so
1663 :			that the plot methods now work.
1664 :
1665 :	bates	1230	2006-03-16 Douglas Bates <bates@bates2>
1666 :
1667 :			* src/dpoMatrix.c (dpoMatrix_chol): Require n > 0 in call to
1668 :			dpotrf - otherwise the BLAS on Mac OS X complains and quits.
1669 :
1670 :			* DESCRIPTION (Date): New release
1671 :
1672 :	maechler	1228	2006-03-15 Martin Maechler <maechler@stat.math.ethz.ch>
1673 :
1674 :			* DESCRIPTION (Version): 0.995-6 -- to be released to CRAN
1675 :
1676 :			* data/KNex.rda: replacing 'mm' and 'y' by KNex <- list(mm=mm, y=y)
1677 :			* man/KNex.Rd: and other help files
1678 :			* tests/*.R: several ones needed adaption
1679 :	bates	1352	* inst/doc/Comparisons.Rnw: ditto
1680 :	maechler	1228
1681 :	maechler	1226	2006-03-11 Martin Maechler <maechler@stat.math.ethz.ch>
1682 :
1683 :			* R/dgCMatrix.R (replCmat): "[<-" methods for dgCMatrix
1684 :
1685 :			* tests/indexing.R: tests for new [<- methods for sparse matrices.
1686 :
1687 :			2006-03-10 Martin Maechler <maechler@stat.math.ethz.ch>
1688 :
1689 :			* R/dgTMatrix.R (replTmat): "[<-" methods for dgTMatrix
1690 :
1691 :			* R/Tsparse.R (.ind.prep): fix out-of-range indexing
1692 :
1693 :			2006-03-08 Martin Maechler <maechler@stat.math.ethz.ch>
1694 :
1695 :			* R/dMatrix.R: enable things like M [ M < 10 ]
1696 :			* R/dgeMatrix.R: implement it
1697 :
1698 :	maechler	1222	2006-03-06 Martin Maechler <maechler@stat.math.ethz.ch>
1699 :
1700 :			* R/AllClass.R: define "summary.mer" and "*.lmer"
1701 :			* R/lmer.R (summary): summary(<mer>) computes & returns the above;
1702 :			* R/lmer.R (show): now works with summary()
1703 :
1704 :			2006-03-04 Martin Maechler <maechler@stat.math.ethz.ch>
1705 :
1706 :			* R/dgCMatrix.R: finally direct "Arith" dgC o dgC
1707 :			* R/Auxiliaries.R (WhichintersectInd): and other utilities to
1708 :			support the above
1709 :
1710 :	bates	1213	2006-02-07 Douglas Bates <bates@stat.wisc.edu>
1711 :
1712 :			* R/lmer.R (lmer): fix initial values of offset and weights for glm.fit.
1713 :			Use glmFit$prior.weights for weights in a glmm.
1714 :			Allow an option usePQL = FALSE to skip the PQL steps for the
1715 :			Laplace method (and, in time, the AGQ method).
1716 :
1717 :			* src/lmer.c (mer_factor): Move downdating and factoring of XtX
1718 :			into a separate function internal_mer_Xfactor to be able to call
1719 :			it from internal_bhat.
1720 :
1721 :	maechler	1200	2006-01-23 Martin Maechler <maechler@stat.math.ethz.ch>
1722 :
1723 :			* tests/Class+Meth.R (tstMatrixClass): function for much better
1724 :			testing; now again of all actual classes.
1725 :
1726 :			* src/Mutils.c (MAKE_TRIANGULAR_BODY, MAKE_SYMMETRIC_BODY):
1727 :			use macros and define make_d_matrix_* and make_i_matrix_*
1728 :			where _i_ is for the ldense routines:
1729 :
1730 :			* src/ldense.c (ltrMatrix_as_lgeMatrix): provide functions
1731 :			* src/ldense.c (lsyMatrix_as_lgeMatrix):
1732 :
1733 :			* R/ldenseMatrix.R: use the above in setAs(*,"lgeMatrix")
1734 :
1735 :
1736 :	maechler	1174	2006-01-16 Martin Maechler <maechler@stat.math.ethz.ch>
1737 :
1738 :			* R/Matrix.R (Matrix): has become much "smarter" now auto-producing
1739 :			many different kinds of matrices.
1740 :			* R/*.R: quite a few new methods were needed for R CMD check with
1741 :			new Matrix(). Very good for users playing around.
1742 :
1743 :
1744 :	maechler	1165	2006-01-15 Martin Maechler <maechler@stat.math.ethz.ch>
1745 :
1746 :			* src/dgeMatrix.c (dMatrix_validate): new
1747 :			* src/Mutils.c (dense_nonpacked_validate): new
1748 :
1749 :			* src/dtrMatrix.c (dtrMatrix_validate): improved/fixed
1750 :
1751 :
1752 :			2006-01-14 Douglas Bates <bates@stat.wisc.edu>
1753 :
1754 :			* R/AllClass.R (compMatrix), (generalMatrix): new virtual classes
1755 :
1756 :	bates	1123	2006-01-07 Douglas Bates <bates@stat.wisc.edu>
1757 :	bates	1119
1758 :	maechler	1127	* DESCRIPTION (Version): 0.99-6 released to CRAN
1759 :
1760 :	bates	1119	* src/dgBCMatrix.c (cscb_trcbsm): Fix due to Peter Dalgaard for
1761 :			segfault in cases with multiple non-nested grouping factors.
1762 :
1763 :	maechler	1109	2006-01-03 Martin Maechler <maechler@stat.math.ethz.ch>
1764 :
1765 :			* DESCRIPTION (Version): 0.99-4 to be released to CRAN
1766 :			(Depends): also on 'utils'
1767 :
1768 :			* R/AllClass.R (diagonalMatrix): new class with "ddi*" and "ldi*"
1769 :			* R/diagMatrix.R (Diagonal): constructor and methods for
1770 :			diagonal matrices
1771 :
1772 :			* R/ltTMatrix.R: new "minimal methods"
1773 :
1774 :	maechler	1091	2005-12-12 Martin Maechler <maechler@stat.math.ethz.ch>
1775 :
1776 :			* R/AllGeneric.R (tcrossprod): 2-argument version; here, and for
1777 :			all methods (and help files).
1778 :
1779 :	maechler	1084	2005-12-09 Martin Maechler <maechler@stat.math.ethz.ch>
1780 :
1781 :			* R/Auxiliaries.R (dimNamesCheck): fixed thinko -> bug
1782 :			for case (dimn. op no_dimn.)
1783 :
1784 :			2005-11-14 Douglas Bates <bates@stat.wisc.edu>
1785 :
1786 :	maechler	1174	* DESCRIPTION (Version): 0.99-2 released to CRAN
1787 :	maechler	1084
1788 :	bates	988	2005-10-21 Douglas Bates <bates@stat.wisc.edu>
1789 :
1790 :			* R/lmer.R (simulate method): Fixed a drop=FALSE problem reported
1791 :			by Julian Faraway.
1792 :
1793 :	maechler	976	2005-10-06 Martin Maechler <maechler@stat.math.ethz.ch>
1794 :
1795 :			* R/Auxiliaries.R (try_as): new utility
1796 :			* R/sparseMatrix.R: use try_as() in coercion to original class
1797 :
1798 :	maechler	956	2005-09-30 Martin Maechler <maechler@stat.math.ethz.ch>
1799 :
1800 :			* src/dgCMatrix.c (double_to_csc): and dgeMatrix_to_csc()
1801 :
1802 :			2005-09-29 Martin Maechler <maechler@stat.math.ethz.ch>
1803 :
1804 :			* R/Auxiliaries.R (dimNamesCheck): added
1805 :
1806 :			* R/Matrix.R (as.array), (as.vector): new
1807 :
1808 :	maechler	954	2005-09-28 Martin Maechler <maechler@stat.math.ethz.ch>
1809 :
1810 :			* R/Matrix.R (Matrix): get logical argument 'sparse' with a smart
1811 :	maechler	956	default.
1812 :			* R/AllClass.R: move 'factors' slot toplevel "Matrix";
1813 :			"pMatrix" now contains "sparseMatrix"
1814 :	maechler	954
1815 :	maechler	948	2005-09-26 Martin Maechler <maechler@stat.math.ethz.ch>
1816 :
1817 :			* tests/Class+Meth.R: new tests; t(t(m)) == m
1818 :
1819 :			* src/dtCMatrix.c (tsc_transpose): add forgotten "diag" slot
1820 :
1821 :			* src/dsTMatrix.c (dsTMatrix_as_dsCMatrix): bad typo (segfault!)
1822 :			* src/dtTMatrix.c (dtTMatrix_as_dtCMatrix): new
1823 :
1824 :			* R/dspMatrix.R: typo in "t" method
1825 :
1826 :	maechler	925	2005-09-18 Douglas Bates <bates@wisc.edu>
1827 :
1828 :			* R/AllClass.R (TsparseMatrix), CsparseM* and RsparseM*
1829 :			* R/Tsparse.R: instead of R/gTMatrix.R
1830 :			* R/Csparse.R: new
1831 :			* src/Tsparse.c (Tsparse_to_Csparse): new; -> cholmod_()
1832 :			* src/Tsparse.c: new; many trivial methods calling cholmod_()
1833 :			* src/Csparse.c (Csparse_to_Tsparse), transpose, (mat|cross)prod:
1834 :			via cholmod
1835 :
1836 :			2005-09-16 Martin Maechler <maechler@stat.math.ethz.ch>
1837 :
1838 :			* R/Auxiliaries.R (non0ind): new function using new C code
1839 :			* src/dgCMatrix.c (compressed_non_0_ij): new utility
1840 :
1841 :	bates	917	2005-09-15 Douglas Bates <bates@localhost.localdomain>
1842 :
1843 :			* src/chm_common.h: header file required by all C sources that
1844 :	maechler	1174	call CHOLMOD functions. It defines a cholmod_common structure
1845 :	bates	917	called 'c' whose address is passed as the last argument to
1846 :			(virtually) every CHOLMOD function.
1847 :
1848 :			* src/Pattern.c: Simple example of the use of CHOLMOD.
1849 :
1850 :			* src/init.c: initialize and finalize the cholmod_common structure.
1851 :
1852 :			* src/Makefile: Added source packages CHOLMOD UMFPACK AMD COLAMD
1853 :			LDL and CCOLAMD from the U. of Florida sparse matrix library.
1854 :
1855 :	maechler	908	2005-09-08 Martin Maechler <maechler@stat.math.ethz.ch>
1856 :
1857 :			* inst/test-tools.R: new file collecting the utility functions used
1858 :			in ./tests/*.R
1859 :
1860 :			* R/ddenseMatrix.R (cbind2): new methods for "numeric" and "matrix"
1861 :			* R/Matrix.R (cbind2): methods for NULL and missing
1862 :
1863 :	maechler	886	2005-08-31 Martin Maechler <maechler@stat.math.ethz.ch>
1864 :
1865 :			* R/AllClass.R: new "index" class for "[" and "[<-":
1866 :			First cut at "symmetricMatrix" and "triangularMatrix"
1867 :			* R/gTMatrix.R (.ind.prep): new function;
1868 :	maechler	1174	Logical and character indexing now work too.
1869 :	maechler	886	* R/Matrix.R: cheap "[<-" methods for denseMatrix now work
1870 :			* tests/indexing.R: new, including *.Rout.save
1871 :			* tests/dgTMatrix.R: new
1872 :
1873 :	bates	876	2005-08-29 Douglas Bates <bates@wisc.edu>
1874 :
1875 :			* src/dgTMatrix.c (graphNEL_as_dgTMatrix): Corrected the position
1876 :			indicator pos not being updated. Also enforced upper triangular
1877 :			for symmetric case. Need to coerce edges component of elements of
1878 :			edge list - grr! (Why don't they define their classes cleanly?)
1879 :
1880 :	maechler	871	2005-08-26 Martin Maechler <maechler@stat.math.ethz.ch>
1881 :
1882 :			* R/Matrix.R: added first "[<-" methods; not yet functional
1883 :	bates	1352	* R/denseMatrix.R: ditto
1884 :	maechler	871	* man/Subassign-methods.Rd: new help file for these
1885 :
1886 :			2005-08-25 Martin Maechler <maechler@stat.math.ethz.ch>
1887 :
1888 :			* DESCRIPTION (Version): 0.98-6
1889 :
1890 :			* R/denseMatrix.R: new file for "[" fallback methods for all dense
1891 :			matrices.
1892 :
1893 :	maechler	868	2005-08-19 Martin Maechler <maechler@stat.math.ethz.ch>
1894 :
1895 :			* src/lgCMatrix.c (lcsc_to_matrix): new; need for
1896 :			as( <logical>, "matrix")
1897 :
1898 :			* R/pMatrix.R: coercion to "lgTMatrix"
1899 :
1900 :			* R/gTMatrix.R: new virtual class to define "[" methods for.
1901 :			* man/gTMatrix-class.Rd:
1902 :			* General slight re-organization of where "[" methods are defined.
1903 :			more to come.
1904 :
1905 :	maechler	871	2005-08-18 Douglas Bates <bates@wisc.edu>
1906 :	maechler	868
1907 :	maechler	1174	* DESCRIPTION (Version): 0.98-5 released to CRAN
1908 :	maechler	871
1909 :			* src/dgTMatrix.c (graphNEL_as_dgTMatrix): add first graphNEL methods
1910 :			* .....
1911 :
1912 :	bates	863	2005-08-18 Douglas Bates <bates@localhost.localdomain>
1913 :
1914 :			* R/lmer.R: Corrected naming scheme in mcmcsamp to work with lmer
1915 :			or glmer objects.
1916 :
1917 :	maechler	860	2005-08-17 Martin Maechler <maechler@stat.math.ethz.ch>
1918 :
1919 :			* DESCRIPTION (Version): 0.98-4 : upload to CRAN
1920 :
1921 :			2005-08-16 Douglas Bates <bates@localhost.localdomain>
1922 :
1923 :			* R/HBMM.R: finish re-writing R-only code.
1924 :
1925 :	bates	854	2005-08-15 Douglas Bates <bates@localhost.localdomain>
1926 :
1927 :			* man/externalFormats.Rd: move documentation for writeHB and
1928 :			writeMM here.
1929 :
1930 :			* src/mmio.c: replace inclusion of <malloc.h> by <stdlib.h>
1931 :			(suggested by Paul Roecker).
1932 :
1933 :			* tests/validObj.R (assertError): Comment out test that is failing
1934 :			after recent changes in r-devel.
1935 :
1936 :	maechler	860
1937 :	maechler	848	2005-08-11 Martin Maechler <maechler@stat.math.ethz.ch>
1938 :
1939 :			* R/AllClass.R: intermediate virtual class "denseMatrix"
1940 :			* man/denseMatrix-class.Rd
1941 :			* NAMESPACE: export it, and also export
1942 :			* man/unused-classes.Rd: "iMatrix", "zMatrix" and "ldenseMatrix"
1943 :
1944 :	bates	846	2005-08-10 Douglas Bates <bates@wisc.edu>
1945 :
1946 :	maechler	848	* DESCRIPTION (Version): 0.98-3 to CRAN
1947 :
1948 :	bates	846	* src/dtrMatrix.c (dtrMatrix_validate): fixed up validation and
1949 :			matrix_solve code (which was really, really wrong).
1950 :
1951 :	bates	835	2005-08-07 Douglas Bates <bates@wisc.edu>
1952 :	maechler	834
1953 :			* DESCRIPTION (Version): 0.98-2
1954 :
1955 :			* R/HBMM.R (readHB), (readMM): read Matrix Market formats
1956 :
1957 :			* R/lmer.R (abbrvNms): new
1958 :			* R/lmer.R (mcmcsamp): allow transformed parameters
1959 :	bates	835	* src/HBMM.c (Matrix_writeMatrixMarket): Added read/write routines
1960 :			for the Harwell-Boeing and the MatrixMarket formats.
1961 :	maechler	834
1962 :			2005-08-04 Martin Maechler <maechler@stat.math.ethz.ch>
1963 :
1964 :			* man/dtrMatrix-class.Rd: add examples
1965 :	bates	835	* man/dtpMatrix-class.Rd: ditto; plus note about PROBLEM
1966 :	maechler	834
1967 :			* TODO: note the dtpMatrix (docu) bug
1968 :
1969 :			* R/zzz.R (.onLoad): assignInNamespace("as.matrix", *, "base")
1970 :			in order to ensure that new as.matrix() is used by old functions,
1971 :			e.g., svd(), qr(), eigen(), dist(),..;
1972 :			apply(), also matplot() or pairs().
1973 :
1974 :
1975 :			2005-08-03 Martin Maechler <maechler@stat.math.ethz.ch>
1976 :
1977 :			* R/lmer.R: add 'fixme' comments and move the linear vs glm check;
1978 :			add comments about 'control' / lmerControl() arguments
1979 :
1980 :	bates	835	2005-07-27 Douglas Bates <bates@wisc.edu>
1981 :	bates	820
1982 :	bates	835	* man/sleepstudy.Rd: Added the sleep data set.
1983 :	maechler	1174	* DESCRIPTION (Version): 0.98-1 released to CRAN
1984 :	bates	820
1985 :	bates	835	2005-07-12 Douglas Bates <bates@wisc.edu>
1986 :	maechler	834	* man/sleepstudy.Rd: Added the sleep data set.
1987 :
1988 :	bates	809	* R/lmer.R (glmmMCMC): Added PACKAGE = "Matrix" in a couple of
1989 :			.Call calls that were producing spurious output.
1990 :
1991 :	bates	835	2005-07-05 Douglas Bates <bates@wisc.edu>
1992 :	bates	801
1993 :			* R/lmer.R (lmer): stored updated variance component estimates in
1994 :			mer object for the generalized model. (Bug reported by Renaud
1995 :			Lancelot).
1996 :
1997 :	bates	835	2005-07-03 Douglas Bates <bates@wisc.edu>
1998 :	bates	794
1999 :			* src/lmer.c (glmer_devAGQ): Added AGQ for single grouping factor,
2000 :			unidimensional case.
2001 :
2002 :	bates	835	2005-06-08 Douglas Bates <bates@wisc.edu>
2003 :	maechler	791
2004 :			* DESCRIPTION (Version): 0.96-1
2005 :
2006 :	maechler	1174	* moved lmer-class' R and C code moved from lme4 to here
2007 :	maechler	791
2008 :	bates	835	2005-06-04 Douglas Bates <bates@wisc.edu>
2009 :	bates	763
2010 :			* R/dgCMatrix.R: Call to csc_matrix_mm used undefined arguments
2011 :			(reported by Guissepe Ragusa <gragusa@ucsd.edu>)
2012 :
2013 :	bates	835	2005-06-02 Douglas Bates <bates@wisc.edu>
2014 :	bates	763
2015 :			* src/Makefile.win: Forgot to update this when Makefile changed.
2016 :
2017 :	bates	835	2005-05-11 Douglas Bates <bates@wisc.edu>
2018 :	bates	726
2019 :			* src/dgCMatrix.c (csc_transpose): Simplified function fixing a
2020 :			bug reported by Kurt Hornik and Michael Hahsler.
2021 :
2022 :	bates	835	2005-05-10 Douglas Bates <bates@wisc.edu>
2023 :	bates	725
2024 :			* src/lgCMatrix.c (Matrix_lgClgCmm): Implementation of methods for
2025 :			logical sparse matrices. These will also be used in the symbolic
2026 :			analysis for lmer objects.
2027 :
2028 :			* src/dsCMatrix.c (dsCMatrix_matrix_solve): Copied the dimensions
2029 :			of b to the result. Fixes bug reported by Jean.Coursol@math.u-psud.fr
2030 :	maechler	791
2031 :	bates	835	2005-05-06 Douglas Bates <bates@wisc.edu>
2032 :	bates	714
2033 :			* src/dgeMatrix.c (dgeMatrix_colsums): Added an implementation of
2034 :			colMeans, colSums, rowMeans and rowSums.
2035 :
2036 :	bates	835	2005-04-18 Douglas Bates <bates@wisc.edu>
2037 :	bates	692
2038 :			* src/lgCMatrix.[ch]: code for _validate method and stub for
2039 :			multiplication operation.
2040 :
2041 :			* src/dgeMatrix.c (dgeMatrix_matrix_solve): Passing wrong argument
2042 :			to dgetrs.
2043 :
2044 :			* src/init.c: Fix cut-and-paste error in definition of
2045 :			dgeMatrix_matrix_solve
2046 :
2047 :			* src/{many files}: Tighten code by using ALLOC_SLOT.
2048 :
2049 :	bates	835	2005-04-15 Douglas Bates <bates@wisc.edu>
2050 :	bates	692
2051 :			* R/AllClass.R: Add lgTMatrix and lgCMatrix classes
2052 :
2053 :			* DESCRIPTION: Eliminate import of stats.
2054 :
2055 :	maechler	791
2056 :	bates	835	2005-04-06 Douglas Bates <bates@wisc.edu>
2057 :	bates	692
2058 :			* R/AllClass.R : add logical sparse matrix classes
2059 :
2060 :	maechler	687	2005-04-01 Martin Maechler <maechler@stat.math.ethz.ch>
2061 :
2062 :			* R/dgTMatrix.R: add "[" method for triplet matrices
2063 :			* R/sparseMatrix.R: and other sparse ones; --> add show() for sparse
2064 :
2065 :	bates	835	2005-03-31 Douglas Bates <bates@wisc.edu>
2066 :	maechler	687
2067 :			* DESCRIPTION (Version): release 0.95-5 to CRAN
2068 :
2069 :			* R/dMatrix.R: add %*%, crossprod and solve "fallback" methods
2070 :			* R/sparseMatrix.R: %*%, crossprod()
2071 :			* R/dgeMatrix.R: more "fallback" methods for numeric/dense matrices
2072 :			* man/*.Rd: move method definitions to 'Matrix' and 'dMatrix'
2073 :			* src/lmer.c (lmer_fitted): fix thinko
2074 :
2075 :	maechler	676	2005-03-26 Martin Maechler <maechler@stat.math.ethz.ch>
2076 :
2077 :			* R/AllClass.R: add two virtual sparse classes ``on top''
2078 :
2079 :			2005-03-24 Martin Maechler <maechler@stat.math.ethz.ch>
2080 :
2081 :			* R/AllClass.R (setClass): use "VIRTUAL" for the virtual classes;
2082 :			correspondingly fix examples and tests/ since new()
2083 :			doesn't work for virtual classes.
2084 :
2085 :	maechler	658	2005-03-17 Martin Maechler <maechler@stat.math.ethz.ch>
2086 :
2087 :			* R/Matrix.R (as.matrix): method and one for unname()
2088 :			* tests/dpoMatrix.R: tests should now be less platform dependent;
2089 :			also run for R 2.1.0; using as.matrix()
2090 :
2091 :	bates	835	2005-03-15 Douglas Bates <bates@wisc.edu>
2092 :	maechler	658
2093 :			* R/pMatrix.R: "pMatrix" class added
2094 :			* ....
2095 :
2096 :	bates	835	2005-03-14 Douglas Bates <bates@wisc.edu>
2097 :	bates	645
2098 :			* R/dtpMatrix.R: Add unpack method and an example.
2099 :
2100 :			* src/dsyMatrix.c (dsyMatrix_trf): Add BunchKaufman factorization
2101 :			of general symmetric matrices and associated S4 methods.
2102 :
2103 :	maechler	658	2005-03-10 Martin Maechler <maechler@stat.math.ethz.ch>
2104 :			+
2105 :			2005-03-05 Martin Maechler <maechler@stat.math.ethz.ch>
2106 :
2107 :			* R/dgeMatrix.R (setAs): and many other files: more coercion,
2108 :			crossprod() and "%*%" methods added; tests, too.
2109 :			* tests/matprod.R: new, for testing these
2110 :
2111 :	bates	835	2005-03-03 Douglas Bates <bates@wisc.edu>
2112 :	bates	599
2113 :			* src/lmer.c (lmer_fitted): Added.
2114 :
2115 :	bates	835	2005-03-02 Douglas Bates <bates@wisc.edu>
2116 :	bates	596
2117 :			* R/dsTMatrix.R: Conversion from dsTMatrix to dsCMatrix
2118 :
2119 :	bates	835	2005-02-28 Douglas Bates <bates@wisc.edu>
2120 :	bates	582
2121 :			* src/*.c,po/,inst/po: Internationalization and localization of
2122 :			the package.
2123 :
2124 :			* src/ldl.[ch]: Removed these as their contents are referenced in the
2125 :			R_ldl.c file.
2126 :
2127 :			* src/flame.[ch]: Removed these source files.
2128 :	maechler	658
2129 :	bates	582	* src/dtrMatrix.c (make_array_triangular): Move to Mutils
2130 :
2131 :			* src/LU.[ch],src/init.c: absorb in factorizations
2132 :
2133 :			* src/Mutils.h: prepare for internationalization
2134 :
2135 :			* src/cblas.h: move the enum definitions to Mutils.h and remove
2136 :			this file
2137 :
2138 :	maechler	578	2005-02-26 Martin Maechler <maechler@stat.math.ethz.ch>
2139 :
2140 :	maechler	579	* R/dgeMatrix.R: provide "dimnames" and "dimnames<-" methods
2141 :
2142 :			* R/dtrMatrix.R: fix t() method
2143 :
2144 :	maechler	578	* R/dgeMatrix.R: define group methods "Arith", "Math", "Math2"
2145 :	maechler	658	* NAMESPACE: export them (and import generics from "methods")
2146 :	maechler	578	* tests/group-methods.R : and test them.
2147 :
2148 :			* src/dtrMatrix.c (dtrMatrix_as_dgeMatrix): prevent seg.fault in
2149 :			border case
2150 :
2151 :			2005-02-24 Douglas Bates <bates@stat.wisc.edu>
2152 :
2153 :	maechler	658	* DESCRIPTION (Version): 0.95-2 released to CRAN
2154 :	maechler	578
2155 :			* src/dgBCMatrix.c:
2156 :			* src/lmer.c: many changes
2157 :			* ...
2158 :
2159 :	maechler	512	2005-02-04 Martin Maechler <maechler@stat.math.ethz.ch>
2160 :
2161 :			* R/Matrix.R: add more sophisticated show() method.
2162 :
2163 :	maechler	578	2005-02-02 Douglas Bates <bates@stat.wisc.edu>
2164 :
2165 :			* */* : almost complete reorganization of classes.
2166 :
2167 :	bates	835	2005-01-26 Douglas Bates <bates@wisc.edu>
2168 :	bates	460
2169 :			* R/AllGeneric.R: Added matrix exponential generic expm and a method
2170 :			for the geMatrix class.
2171 :
2172 :	bates	835	2005-01-24 Douglas Bates <bates@wisc.edu>
2173 :	bates	460
2174 :			* src/Makefile (clean): Remove *.a and *.so
2175 :
2176 :			* man/cscBlocked-class.Rd: Remove reference to the lmer-class.
2177 :
2178 :	bates	835	2005-01-23 Douglas Bates <bates@wisc.edu>
2179 :	bates	460
2180 :	maechler	658	* src/lmer.c (Lind): Definition of Lind was backwards. This only
2181 :	bates	460	had an effect in cases with more than 2 grouping factors.
2182 :
2183 :	bates	835	2005-01-03 Douglas Bates <bates@wisc.edu>
2184 :	bates	415
2185 :			* src/lmeRep.c (lmer_variances): change from lmeRep to lmer
2186 :
2187 :	bates	835	2004-12-23 Douglas Bates <bates@wisc.edu>
2188 :	bates	410
2189 :			* src/init.c (R_init_Matrix): Reorder calls to R_registerRoutines
2190 :			and R_useDynamicSymbols (suggested by B.D.Ripley).
2191 :
2192 :	bates	835	2004-12-14 Douglas Bates <bates@wisc.edu>
2193 :	bates	392
2194 :			* R/sscMatrix.R: Add determinant methods
2195 :
2196 :			* src/triplet.[ch],src/init.c (triplet_to_matrix): Add a coercion
2197 :			for tripletMatrix to matrix.
2198 :
2199 :	bates	835	2004-12-13 Douglas Bates <bates@wisc.edu>
2200 :	bates	388
2201 :	bates	392	* R/AllClass.R (.onLoad): Eliminate the bbCrosstab class, which is
2202 :			no longer used.
2203 :
2204 :	bates	388	* src/R_ldl.c: Created an R-specific version of the ldl.[ch] files
2205 :			with dynamic allocation of scratch arrays.
2206 :
2207 :			* src/ssclme.c (ssclme_copy_ctab): Fixed bug in creation of ZtZ
2208 :			for multivariate random effects with multiple grouping factors.
2209 :			Fixes part but not all of #15.
2210 :
2211 :	bates	835	2004-12-03 Douglas Bates <bates@wisc.edu>
2212 :	bates	375
2213 :			* src/lmeRep.c (lmeRep_factor): order of operations for multiple
2214 :			scalar grouping factors corrected.
2215 :
2216 :	bates	835	2004-11-29 Douglas Bates <bates@wisc.edu>
2217 :	bates	375
2218 :			* src/bCrosstab.c: remove diag_update which is no longer used
2219 :
2220 :	bates	835	2004-11-16 Douglas Bates <bates@wisc.edu>
2221 :	bates	350
2222 :			* src/Metis_utils.c: Move metis.h include to C sources so that the
2223 :			.h file can be included.
2224 :
2225 :	bates	835	2004-11-12 Douglas Bates <bates@wisc.edu>
2226 :	bates	342
2227 :	bates	350	* src/LU.c,geMatrix.c,trMatrix.c, etc.:
2228 :	bates	342	Complete allocation of slots in NEW_OBJECT.
2229 :
2230 :			* src/Mutils.h: Moved list of symbols to an include file
2231 :
2232 :	bates	835	2004-11-11 Douglas Bates <bates@wisc.edu>
2233 :	bates	342
2234 :			* src/geMutils.c (Matrix_init): remove unused function
2235 :
2236 :	bates	835	2004-11-10 Douglas Bates <bates@wisc.edu>
2237 :	bates	342
2238 :			* src/cscMatrix.c (csc_to_imagemat): removed unused function
2239 :
2240 :	bates	835	2004-11-05 Douglas Bates <bates@wisc.edu>
2241 :	bates	327
2242 :			* src/Makefile.win (SOURCES_C): Keep consistent with Makefile
2243 :
2244 :	bates	835	2004-10-27 Douglas Bates <bates@wisc.edu>
2245 :	bates	303
2246 :			* R/pdmatrix.R: remove PACKAGE="Matrix" in .Call calls
2247 :
2248 :	bates	835	2004-10-04 Douglas Bates <bates@wisc.edu>
2249 :	bates	296
2250 :			* src/init.c: Created R_init_Matrix and added registration of C
2251 :			routines.
2252 :
2253 :	bates	835	2004-10-02 Douglas Bates <bates@wisc.edu>
2254 :	bates	283
2255 :			* R/tripletMatrix.R: Force a require(lattice) for the image methods.
2256 :
2257 :	bates	835	2004-06-15 Douglas Bates <bates@wisc.edu>
2258 :	bates	229
2259 :			* man/trMatrix-class.Rd: Escape the % chars in .Rd files.
2260 :
2261 :	bates	111	2004-04-20 Douglas Bates <bates@stat.wisc.edu>
2262 :
2263 :			* src/Makefile.win ($(SHLIB)): Modifications per Uwe Ligges.
2264 :
2265 :	bates	109	2004-04-19 Douglas Bates <bates@stat.wisc.edu>
2266 :
2267 :			* src/ssclme.c (ssclme_update_mm): fix logic error in
2268 :			ssclme_update_mm
2269 :
2270 :	bates	105	2004-04-18 Douglas Bates <bates@stat.wisc.edu>
2271 :
2272 :			* src/ssclme.c (ssclme_coef, ssclme_coefGets): Create consistency
2273 :			in the order of unconstrained and constrained parameters.
2274 :			(ssclme_gradient): Added the gradients (not yet correct for
2275 :			multidimensional, unconstrained case).
2276 :
2277 :	bates	78	2004-04-14 Douglas Bates <bates@stat.wisc.edu>
2278 :
2279 :			* src/ssclme.c (ssclme_EMsteps): Fix logic in REML update
2280 :
2281 :			* src/Makefile.win: Remove unneeded ranlib call
2282 :
2283 :	bates	71	2004-04-12 Douglas Bates <bates@stat.wisc.edu>
2284 :
2285 :			* DESCRIPTION (Version): New release
2286 :
2287 :			* src/Makefile.win: Update Makefile.win to umfpack removal.
2288 :
2289 :	bates	49	2004-04-05 Douglas Bates <bates@bates2_home>
2290 :
2291 :			* src/triplet_to_col.c: Create triplet_to_col as a native
2292 :	maechler	658	function, not the version from umfpack. There were problems with
2293 :	bates	49	the configuration of UMFPACK for 64-bit processors and there was
2294 :			only one umfpack routine being used so I moved it here.
2295 :
2296 :	bates	45	2004-04-04 Douglas Bates <bates@bates2_home>
2297 :
2298 :			* src/ssclme.c (ssclme_variances): New function.
2299 :
2300 :	bates	28	2004-03-28 Douglas Bates <bates@bates2_home>
2301 :
2302 :			* src/ssclme.c (ssclme_fitted): Added function.
2303 :
2304 :	bates	22	2004-03-27 Douglas Bates <bates@bates2_home>
2305 :
2306 :			* src/ssclme.c (ssclme_transfer_dimnames): Add new function to
2307 :			store the dimnames in the XtX and bVar slots
2308 :			(ssclme_update_mm): Change the dimensions of the bVar slot
2309 :			components and the returned value from ssclme_ranef.
2310 :
2311 :	bates	10	2004-03-18 Douglas Bates <bates@stat.wisc.edu>
2312 :
2313 :			* R/{pdMat.R,pdIdent.R,pdLogChol.R,pdMatrixLog.R,pdNatural.R},
2314 :			src/{pdMat.c,pdIdent.c,pdLogChol.c,pdNatural.c},
2315 :			tests/{pdCompSymm.R,pdDiag.R,pdIdent.R,pdLogChol.R,pdNatural.R},
2316 :			man/{pdMat-class.Rd,pdmatrix-class.Rd,corrmatrix-class.Rd,
2317 :			pdDiag-class.Rd,pdIdent-class.Rd,pdNatural-class.Rd,
2318 :			pdLogChol-class.Rd,coefGets.Rd,pdCompSymm-class.Rd,
2319 :			pdfactor-class.Rd,pdFactor.Rd,pdMatrix.Rd,
2320 :			pdBlocked-class.Rd},AllClass.R,AllGeneric.R:
2321 :			Moved the pdMat classes from the lme4 package.
2322 :
2323 :			2004-03-02 Douglas Bates <bates@stat.wisc.edu>
2324 :
2325 :			* man/ssclme-class.Rd: Update definition and documentation of the
2326 :			ssclme class to include the DIsqrt slot.
2327 :
2328 :			* src/ssclme.c (ssclme_deviance): Modify order of computation
2329 :			(much faster using dsyrk, a level 3 BLAS routine).
2330 :
2331 :			* src/Makefile (SUBLIBS): Change definition (K. Hornik)
2332 :
2333 :			2004-02-28 Douglas Bates <bates@stat.wisc.edu>
2334 :
2335 :			* tests/ssclme.R: Modify the test to account for the permutation
2336 :			of the levels of the grouping factors.
2337 :
2338 :			2004-02-23 Douglas Bates <bates@stat.wisc.edu>
2339 :
2340 :			* R/ssclme.R,src/ssclme.c (ssclme): Move slots of sscCrosstab slot
2341 :			directly into the ssclme class definition.
2342 :
2343 :			2004-02-22 Douglas Bates <bates@stat.wisc.edu>
2344 :
2345 :			* DESCRIPTION (Date): New release
2346 :
2347 :			* man/ssclme-class.Rd: new file.
2348 :
2349 :			* src/ssclme.c (ssclme_loglik): major revisions in design. It
2350 :			works and it's fast!
2351 :
2352 :			2004-02-17 Douglas Bates <bates@stat.wisc.edu>
2353 :
2354 :			* src/taucs/Makefile.win (lib): Change "ar" to "$(AR)" (B.Ripley)
2355 :
2356 :			2004-02-16 Douglas Bates <bates@stat.wisc.edu>
2357 :
2358 :			* DESCRIPTION (Date): New release
2359 :
2360 :			* NAMESPACE: Don't export ssclme.
2361 :
2362 :			* data/ScotsSec.rda, man/ScotsSec.Rd: Add Scottish secondary
2363 :			school data.
2364 :
2365 :			2004-02-11 Douglas Bates <bates@stat.wisc.edu>
2366 :
2367 :			* src/sscCrosstab.c (sscCrosstab): Added a row to the incidence to
2368 :			keep track of the fixed-effects and the response. Counts also
2369 :			gets an extra element, which is always one.
2370 :
2371 :			* src/ldl.c: Include these routines from Tim Davis' LDL package.
2372 :
2373 :			2004-02-10 Douglas Bates <bates@stat.wisc.edu>
2374 :
2375 :			* src/cscMatrix.c (csc_transpose): new function
2376 :
2377 :			* src/Mutils.c (csc_sort_columns): perm/iperm confusion corrected
2378 :			(csc_components_transpose): new function
2379 :
2380 :			2004-02-06 Douglas Bates <bates@stat.wisc.edu>
2381 :
2382 :			* src/triplet.c (triplet_validate): Fix Dim slot on generated
2383 :			triplets
2384 :
2385 :			2004-01-30 Douglas Bates <bates@stat.wisc.edu>
2386 :
2387 :			* R/sscCrosstab.R (sscCrosstab): Added sscCrosstab generator function.
2388 :
2389 :			* src/LU.h (MATRIX_LU_H): Add #ifndef #define ... #endif to this
2390 :			and all other .h files in src.
2391 :
2392 :			* src/Makefile.win: This and other Makefile.win files contributed
2393 :			by Brian Ripley.
2394 :
2395 :			2004-01-27 Douglas Bates <bates@stat.wisc.edu>
2396 :
2397 :			* R/syMatrix.R: Added methods for "%*%".
2398 :
2399 :			* R/Hilbert.R (Hilbert): Changed Hilbert function to return a
2400 :			poMatrix object.
2401 :
2402 :			2004-01-26 Douglas Bates <bates@stat.wisc.edu>
2403 :
2404 :			* man/sscChol-class.Rd,man/mm.Rd,man/y.Rd: Added man pages.
2405 :
2406 :			2004-01-25 Douglas Bates <bates@bates2_home>
2407 :
2408 :			* inst/doc/Introduction.Rnw,Comparisons.Rnw: Added vignettes.
2409 :
2410 :			* R/csc.R: Convert all cscMatrix classes to use Dim slot instead
2411 :			of nrow.
2412 :
2413 :			2003-12-31 Douglas Bates <bates@stat.wisc.edu>
2414 :
2415 :			* src/taucs/taucs.h: Moved taucs.h, amd.h, and umfpack.h into
2416 :			subdirectories.
2417 :
2418 :			2003-12-08 Douglas Bates <bates@stat.wisc.edu>
2419 :
2420 :			* src/taucs.h: Accidently referred to global header files
2421 :			instead of local files.
2422 :
2423 :			2003-12-04 Douglas Bates <bates@stat.wisc.edu>
2424 :
2425 :			* R/AllClass.R: Lots of changes. Removed all the lapack++ code
2426 :			and methods and replaced all classes with S4 classes.
2427 :
2428 :			2003-04-19 Douglas Bates <bates@stat.wisc.edu>
2429 :
2430 :			* R/det.R,man/det.Rd: Change name of det generic to determinant
2431 :
2432 :			* src/R_LapackPP.cc: Change method of calculating determinants
2433 :
2434 :			2003-02-03 Douglas Bates <bates@stat.wisc.edu>
2435 :
2436 :			* DESCRIPTION (Version): removed empty data directory as requested
2437 :			by CRAN maintainers. Changed version number and date.
2438 :
2439 :			2002-10-23 Douglas Bates <bates@stat.wisc.edu>
2440 :
2441 :			* src/laindex.h: Applied patches from Brian Ripley for compilation
2442 :			under Windows.
2443 :
2444 :			* Added configure.win and src/Makevars.win as requested by Brian
2445 :			Ripley.
2446 :
2447 :			2002-05-03 Douglas Bates <bates@stat.wisc.edu>
2448 :
2449 :			* src/lamatrix.h: Removing pre-1.2.0 compatibility code per Kurt
2450 :			Hornik.
2451 :
2452 :			2002-04-24 Douglas Bates <bates@stat.wisc.edu>
2453 :
2454 :			* configure.ac: Replaced configure.in with configure.ac
2455 :			contributed by Kurt Hornik.
2456 :
2457 :			* aclocal.m4 (ac_clean_files): Replaced this with Kurt Hornik's
2458 :			version for R-1.5.0
2459 :
2460 :	maechler	512
2461 :	bates	10	2001-12-10 Douglas Bates <bates@stat.wisc.edu>
2462 :
2463 :			* man/eigen.Rd: Removed the .Alias in the example

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