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Annotation of /pkg/ChangeLog

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

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