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Annotation of /pkg/ChangeLog

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Revision 2139 - (view) (download)

1 : maechler 2139 2008-03-18 Martin Maechler <maechler@stat.math.ethz.ch>
2 :    
3 :     * src/UFsparse_download.sh: -->
4 :     * src/CHOLMOD/: update to CHOLMOD version 1.6 (Nov.2007)
5 :    
6 : maechler 2137 2008-03-17 Martin Maechler <maechler@stat.math.ethz.ch>
7 :    
8 :     * src/dsCMatrix.c (dsCMatrix_LDL_D): even faster utility with same
9 :     functionality; barely tested in
10 :     * tests/factorizing.R
11 :    
12 :     * src/Csparse.c (diag_tC): new functionality to enable faster
13 :     determinant(<dsCMatrix>, .) in
14 :     * R/dsCMatrix.R
15 :    
16 :     2008-03-17 18:53 Douglas Bates <bates@stat.wisc.edu>
17 :    
18 :     * R/CHMfactor.R, inst/include/Matrix.h, inst/include/Matrix_stubs.c,
19 :     src/CHMfactor.c, src/CHMfactor.h,
20 :     man/CHMfactor-class.Rd, src/init.c, tests/factorizing.R:
21 :     Log-determinant of the parent matrix from a CHMfactor object as
22 :     chm_factor_ldetL2; documentation and support
23 :    
24 :     2008-03-15 Martin Maechler <maechler@stat.math.ethz.ch>
25 :    
26 :     * R/dsCMatrix.R: enable determinant(<dsCMatrix>, .) via chol(.)
27 :    
28 : maechler 2130 2008-03-14 Martin Maechler <maechler@stat.math.ethz.ch>
29 :    
30 :     * R/dsCMatrix.R: setAs(., "dsCMatrix") but with a deprecation
31 :     warning.
32 :    
33 : maechler 2128 2008-03-13 Martin Maechler <maechler@stat.math.ethz.ch>
34 :    
35 :     * DESCRIPTION (Version, Date): bug-fix release 0.999375-6
36 :    
37 :     * R/diagMatrix.R (diag2tT.u): utility to be smarter in
38 :     <diagonal> o <sparse_triangular>
39 :     setAs(., "nMatrix") added.
40 :    
41 :     * R/diagMatrix.R (Diagonal): Diagonal(4, x=3) now works too
42 :    
43 :     * R/Auxiliaries.R (.diagU2N): more careful coercion in 2 steps
44 :     new argument 'checkDense = FALSE'.
45 :    
46 :    
47 : maechler 2125 2008-03-07 Martin Maechler <maechler@stat.math.ethz.ch>
48 :    
49 : maechler 2127 * src/dgeMatrix.c (dgeMatrix_exp): fix the octave-origin bug in the
50 :     back-permutation of the matrix exponential.
51 :    
52 :     * tests/matr-exp.R: test the fix (for an example where expm() was wrong).
53 :    
54 : maechler 2126 * DESCRIPTION (Date,Version): ready to release 0.999375-5
55 :    
56 : maechler 2125 * tests/simple.R: testing diagN2U
57 :    
58 :     2008-03-06 Martin Maechler <maechler@stat.math.ethz.ch>
59 :    
60 :     * R/Auxiliaries.R (diagN2U): interface to
61 :    
62 :     * src/Csparse.c (Csparse_diagN2U): .Call()able SEXP version of chm_diagN2U()
63 :    
64 :     * tests/matprod.R: test for triangularity preserving <dtC> %*% <dtC>
65 :    
66 : maechler 2123 2008-03-05 Martin Maechler <maechler@stat.math.ethz.ch>
67 :    
68 : maechler 2125 * src/chm_common.c (chm_diagN2U): new utility.
69 :    
70 :     * src/Csparse.c (Csparse_Csparse_crossprod, Csparse_Csparse_prod):
71 :     make use of chm_diagN2U() and hence now preserve triangularity and
72 :     unit-triangularity.
73 :    
74 : maechler 2123 * DESCRIPTION (LicenseDetails): new; such that 'License:' becomes "canonical"
75 :    
76 : maechler 2120 2008-03-04 Martin Maechler <maechler@stat.math.ethz.ch>
77 :    
78 :     * R/diagMatrix.R (subDiag): fix when x[..] became a vector
79 :    
80 :     * src/Tsparse.c (Tsparse_diagU2N): new utility, necessary for e.g.
81 :     * src/Csparse.c (Csparse_crossprod): use [CT]sparse_diagU2N() !!
82 :    
83 :     * R/Auxiliaries.R (.diagU2N): make use of new Tsparse_diagU2N
84 :    
85 :     * R/Ops.R ("-" (<sparseMatrix>)): use diagU2N()
86 :    
87 :     * src/chm_common.c (AS_CHM_FINISH): add note about problem
88 :     for triangular (diag = "U").
89 :    
90 : maechler 2115 2008-02-21 Martin Maechler <maechler@stat.math.ethz.ch>
91 :    
92 :     * R/Auxiliaries.R (as_Csparse2): drop this, replacing by
93 :     * R/bind.R: .Call(dense_to_Csparse, *)
94 :    
95 :     2008-02-20 Martin Maechler <maechler@stat.math.ethz.ch>
96 :    
97 :     * R/Matrix.R (Matrix): no longer use coercions to specific classes
98 :     (since we are discouraging them in user code).
99 :    
100 :     * tests/*.R: also replaces coercions to specific classes by
101 :     coercions to super classes.
102 :    
103 :     * R/denseMatrix.R (.dense2C): simplified by using forceSymmetric()
104 :    
105 :    
106 :     2008-02-19 Martin Maechler <maechler@stat.math.ethz.ch>
107 :    
108 :     * man/CAex.Rd: example: coerce to symmetric*, not dsC*
109 :    
110 :     * src/dense.c (dense_band): generalized from ddense_band
111 :    
112 :     * R/ddenseMatrix.R (.trilDense,.triuDense, .bandDense):
113 :     now for "denseMatrix" (instead of just "ddense*"); much
114 :     simplified setMethod()s for these.
115 :    
116 :     * src/dense.c (dense_to_symmetric): generalized from ddense_*
117 :    
118 :     2008-02-18 Martin Maechler <maechler@stat.math.ethz.ch>
119 :    
120 :     * R/AllGeneric.R: forceSymmetric() generic: fast no-checking
121 :     version of as(*, "symmetricMatric").
122 :    
123 :     * src/dense.c (ddense_to_symmetric): add 'symm_test' argument, and
124 :     * R/symmetricMatrix.R: set it TRUE in coercion to "symmetricMatrix"
125 :    
126 : maechler 2113 2008-02-16 Martin Maechler <maechler@stat.math.ethz.ch>
127 :    
128 :     * R/Matrix.R (subset.ij): utility, as first step to faster
129 :     M [ <ij-matrix> ] indexing.
130 :    
131 :     * R/Matrix.R (.M.sub.i.logical): M[ <logical> ] : try better.
132 :    
133 :     * src/dense.c (ddense_symmpart, ddense_skewpart): new functions
134 :     for more efficient symmpart() and skewpart() methods.
135 :    
136 :     * src/Mutils.c (equal_string_vectors): utility
137 :    
138 :     * src/dense.c (ddense_to_symmetric): new function used in
139 :    
140 :     * R/symmetricMatrix.R: setAs(., "symmetricMatrix")
141 :    
142 :     * R/sparseMatrix.R, et_al (isSymmetric): add '...' to formals, in
143 :     order to match the generic (and evade .local(..)).
144 :    
145 :     * R/dsCMatrix.R: dgC -> dsC: use C code!
146 :    
147 :     * NAMESPACE, R/AllGeneric.R (symmpart, skewpart): new functions
148 :     as per TODO
149 :    
150 :     * R/Auxiliaries.R (setZero, all0Matrix): new utilities
151 :    
152 :     * R/symmetricMatrix.R: obvious symmpart(), skewpart() methods
153 :    
154 :    
155 :     2008-02-15 Martin Maechler <maechler@stat.math.ethz.ch>
156 :    
157 :     * R/Ops.R (.Arith.Csparse): use diagU2N when needed in triangular
158 :    
159 :     * R/Auxiliaries.R (non0.i): take out of non0ind
160 :    
161 :     * R/ddenseMatrix.R (.trilDense, .triuDense, .bandDense):
162 :     make tril(), triu(), band() work for "matrix" and all "dense*"
163 :    
164 :     * R/triangularMatrix.R (.tri[lu].tr): need .diagU2N(*)
165 :     * tests/simple.R: test the fix above
166 :    
167 :     * R/sparseMatrix.R ([): simplification: no coerce to <general>
168 :     before we use as(., <Tsparse>)[...] anyway
169 :    
170 :     * R/Rsparse.R (.viaC.to.R): mostly instead of .viaC.to.dgR()
171 :    
172 :     * R/triangularMatrix.R (isTriangular): methods for all subclasses
173 :     instead of "triangularMatrix" -- just to disambiguate
174 :    
175 :     2008-02-14 Martin Maechler <maechler@stat.math.ethz.ch>
176 :    
177 :     * tests/Class+Meth.R (dotestMat): add m[FALSE, FALSE] { <-> TODO}
178 :     * tests/indexing.R: example that fails above
179 :    
180 : maechler 2110 2008-01-26 Martin Maechler <maechler@stat.math.ethz.ch>
181 :    
182 :     * R/Matrix.R (.M.sub.i.2col): fix for logical matrix indexing
183 :     * R/Tsparse.R (.TM.sub.i.2col, .TM.repl.i.2col): ditto;
184 :     now, M[lower.tri(M)] and M[lower.tri(M)] <- v work better
185 :    
186 :     * src/Tsparse.c (Tsparse_to_tCsparse): new fast utility.
187 :     * src/Tsparse.h, init.c: ditto
188 :     * R/Auxiliaries.R (isTriT): new; faster than going via Csparse
189 :     both isTriC() and isTriT() now return TRUE with "kind" or FALSE.
190 :     * R/sparseMatrix.R (isTriangular): hence simplified
191 :    
192 : maechler 2108 2008-01-24 Martin Maechler <maechler@stat.math.ethz.ch>
193 :    
194 :     * R/Ops.R (.Arith.Csparse): new utility factored out of former
195 :     <dgC> o <dgC>, extended for triangular and also used in <dtC> o <dtC>.
196 :    
197 : maechler 2106 2008-01-23 Martin Maechler <maechler@stat.math.ethz.ch>
198 :    
199 :     * tests/factorizing.R (checkSchur): and more tests for checking Schur()
200 :    
201 : maechler 2108 * inst/test-tools.R (isOrthogonal): new function; also file restructured
202 : maechler 2106
203 :     2008-01-22 Martin Maechler <maechler@stat.math.ethz.ch>
204 :    
205 :     * R/ngTMatrix.R: allow as(<numeric matrix>, "ngTMatrix") and hence
206 :     coercion to "nMatrix" and "pMatrix"
207 :    
208 :     * R/AllClass.R: "Schur" class; "number" class union
209 :     * man/number-class.Rd:
210 :     * man/Schur-class.Rd:
211 :    
212 :     * R/eigen.R (.dgeSchur): utility, and return "Schur" class
213 :     (.simpleSchur): Schur() method for diagonal matrices
214 :     (.triSchur): Schur() method for triangular matrices
215 :     (Schur.sym): Schur() for symmetric matrices {building on eigen()}.
216 :    
217 :    
218 :     2008-01-21 Martin Maechler <maechler@stat.math.ethz.ch>
219 :    
220 :     * src/dgCMatrix.c (dgCMatrix_QR): set @Dim slot (as per doc)
221 :    
222 : maechler 2105 2008-01-15 Martin Maechler <maechler@stat.math.ethz.ch>
223 :    
224 :     * R/CHMfactor.R (solve): method for b="numeric", but also b="ANY"
225 :     in order to ensure 'system = *' is not lost;
226 :     formals()$system instead of cut&paste.
227 :     * tests/factorizing.R: test solve(<CHM..>, <numeric>)
228 :    
229 : maechler 2102 2008-01-11 Martin Maechler <maechler@stat.math.ethz.ch>
230 : maechler 2096
231 : maechler 2105 * DESCRIPTION (Date): make ready for release --> 0.999375-4
232 : maechler 2096
233 : maechler 2102 * R/dgeMatrix.R: fix rcond() method for "dgeMatrix".
234 : maechler 2096
235 : maechler 2098 2007-12-08 Martin Maechler <maechler@stat.math.ethz.ch>
236 : maechler 2096
237 : maechler 2098 * R/pMatrix.R: as(*, "matrix") now returns 0/1 *integer* matrix,
238 :     and hence does as.vector(.).
239 :     * man/pMatrix-class.Rd: docs
240 :     * R/sparseMatrix.R: fix for printing "integer sparse"
241 :    
242 :     * tests/Class+Meth.R (tstMatrixClass): test M[FALSE], M[2] etc
243 :    
244 :     * R/Matrix.R and others: use "exact" function argument list for
245 :     both "[" : (x, i,j, ..., drop)
246 :     and "[<-" : (x, i,j, ..., value)
247 :    
248 :     * R/denseMatrix.R: M[i] and M[i] <- v (i vector) now work
249 :     * R/Tsparse.R (replTmat): ditto
250 :     * R/diagMatrix.R (replDiag): ditto
251 :     * R/Csparse.R (replCmat): ditto {was it worth the pain?}
252 :     * tests/indexing.R: testing the above
253 :    
254 : maechler 2096 2007-12-07 Martin Maechler <maechler@stat.math.ethz.ch>
255 :    
256 :     * R/sparseMatrix.R (cov2cor): method for sparse matrices
257 :    
258 :     * R/diagMatrix.R ([<-): fix D[ cbind(i,j) ] <- v
259 :    
260 :     * R/bind2.R: fix for Rsparse* and rbind2(dense,dense)
261 :    
262 :     * tests/Class+Meth.R: test cbind2, rbind2 and diag<-
263 :    
264 :     2007-12-06 Martin Maechler <maechler@stat.math.ethz.ch>
265 :    
266 :     * R/Matrix.R: "generic" cov2cor() method
267 :    
268 :     * R/nearPD.R: new 'only.values', 'keepDiag' arguments;
269 :     speed up Q %*% D %*% t(Q)
270 :     * tests/dpoMatrix.R: test nearPD()
271 :    
272 :     2007-12-05 Doug Bates and Martin Maechler
273 :    
274 :     * R/sparseMatrix.R: xtabs(*, sparse=.) function; an extention of
275 :     stats::xtabs() allowing to create sparse matrices.
276 :    
277 :     2007-10-08 Martin Maechler <maechler@stat.math.ethz.ch>
278 :    
279 :     * DESCRIPTION (Version): *-4 (released *-3 two days ago)
280 :    
281 : maechler 2081 2007-10-06 Martin Maechler <maechler@stat.math.ethz.ch>
282 :    
283 :     * R/pMatrix.R: solve(<Matrix>, <pMatrix>)
284 :    
285 :     2007-10-05 Martin Maechler <maechler@stat.math.ethz.ch>
286 :    
287 :     * R/LU.R: solve() method for "denseLU"
288 :    
289 :     2007-10-01 Martin Maechler <maechler@stat.math.ethz.ch>
290 :    
291 :     * DESCRIPTION (Version): 0.999375-3 preparing for release
292 :    
293 :     * R/AllGeneric.R: simplify if(.) .. else .. for R <= 2.5.1
294 :    
295 :     * R/Matrix.R (Matrix): .Internal(matrix(..)) different for R >= 2.7.0
296 :    
297 : maechler 2073 2007-09-26 Martin Maechler <maechler@stat.math.ethz.ch>
298 :    
299 :     * R/pMatrix.R (.m.mult.pMat): fix <matrix> %*% <pMatrix>,
300 :     thanks to Kasper Kristensen.
301 :     * tests/matprod.R: regression test for that.
302 :    
303 : bates 2069 2007-09-23 17:32 Douglas Bates <bates@stat.wisc.edu>
304 :    
305 :     * [r4778] R/AllGeneric.R: Check R version before defining generics for
306 :     primitives
307 :    
308 : maechler 2073 2007-09-13 Martin Maechler <maechler@stat.math.ethz.ch>
309 :    
310 :     * R/denseMatrix.R (rcond): method
311 :     * R/sparseQR.R (rcond): method, use x or t(x)
312 :    
313 :     2007-09-12 Martin Maechler <maechler@stat.math.ethz.ch>
314 :    
315 :     * R/dgeMatrix.R (rcond): method: work via qr.R() for non-square
316 :     matrices.
317 :     * R/sparseMatrix.R: Ditto for all other rcond() method definitions.
318 :    
319 :     * man/rcond.Rd: mention the more general definition, and add
320 :     example for non-square matrices.
321 :    
322 :     * man/chol.Rd: new file, for the S4 chol() generic and all methods.
323 :    
324 :     2007-09-11 Martin Maechler <maechler@stat.math.ethz.ch>
325 :    
326 :     * R/sparseQR.R: add qr.R() method [to be used for rcond()]
327 :    
328 : maechler 2062 2007-09-01 Martin Maechler <maechler@stat.math.ethz.ch>
329 :    
330 :     * R/Matrix.R ([<-): add (Matrix,missing,ANY,Matrix) etc
331 :     * tests/indexing.R: add new regression for the above cases.
332 :    
333 : maechler 2061 2007-08-30 Martin Maechler <maechler@stat.math.ethz.ch>
334 :    
335 :     * src/Mutils.h (__sun): clause for alloca.h on Solaris
336 :    
337 : maechler 2056 2007-08-16 Martin Maechler <maechler@stat.math.ethz.ch>
338 :    
339 :     * DESCRIPTION (Date, Version): 0.999375-2
340 :    
341 :     2007-08-15 Martin Maechler <maechler@stat.math.ethz.ch>
342 :    
343 :     * R/HBMM.R (readMM): make work for pattern matrices as well
344 :    
345 : bates 2050 2007-08-14 13:07 Douglas Bates <bates@stat.wisc.edu>
346 :    
347 :     * [r4730] src/Mutils.h: declare alloca
348 :     * [r4734] NAMESPACE, R/AllGeneric.R, R/Csparse.R, R/HBMM.R, R/Tsparse.R,
349 :     R/dgCMatrix.R, R/dgTMatrix.R, R/dsCMatrix.R, R/dsTMatrix.R,
350 :     man/externalFormats.Rd, src/Csparse.c, src/Csparse.h, src/DEPS.mkf,
351 :     src/HBMM.c, src/HBMM.h, src/Mutils.h, src/SOURCES_C.mkf, src/init.c,
352 :     src/mmio.c, src/mmio.h: Remove deprecated function writeHB and its
353 :     methods; switch writeMM to use CHOLMOD code; repair readMM
354 :    
355 : maechler 2048 2007-08-14 Martin Maechler <maechler@stat.math.ethz.ch>
356 :    
357 :     * R/nearPD.R, man/nearPD.Rd (nearPD): new function built on Jens
358 :     Oehlschlaegel's ... result type still to be discussed!
359 :    
360 : maechler 2043 2007-08-10 Martin Maechler <maechler@stat.math.ethz.ch>
361 :    
362 :     * man/image-methods.Rd: new, combining all image() methods
363 :    
364 :     2007-08-09 Martin Maechler <maechler@stat.math.ethz.ch>
365 :    
366 :     * R/dgCMatrix.R: define qr() and lu() methods for "sparseMatrix"
367 :     to work via dgC...
368 :    
369 :     * R/Matrix.R (Matrix): special treatment for "table" (S3)
370 :    
371 :     2007-08-07 Martin Maechler <maechler@stat.math.ethz.ch>
372 :    
373 :     * R/dgTMatrix.R (image): change defaults to
374 :     aspect = "iso", colorkey = FALSE
375 :    
376 : maechler 2039 2007-08-06 Martin Maechler <maechler@stat.math.ethz.ch>
377 :    
378 :     * src/dsyMatrix.c (dsyMatrix_matrix_mm): 'b' might be matrix;
379 :     must copy its *expanded* x slot before LAPACK call.
380 :    
381 :     * tests/matprod.R: test the last days' changes.
382 :    
383 : bates 2041 2007-08-06 16:43 Douglas Bates <bates@stat.wisc.edu>
384 :    
385 :     * [r4712] inst/include/Matrix_stubs.c: Change R_cholmod_printf in stubs
386 :     as well as in sources
387 : bates 2050 * [r4713] src/dsyMatrix.c: Duplicate the contents of the RHS before
388 :     Lapack call
389 : maechler 2043
390 : maechler 2036 2007-08-03 Martin Maechler <maechler@stat.math.ethz.ch>
391 :    
392 :     * R/Matrix.R (%*%, crossprod, tcrossprod): add method for
393 : maechler 2039 ("Matrix", "matrix") which is needed in some cases.
394 :     Ditto for solve().
395 : maechler 2036
396 :     * R/colSums.R (.as.dge.Fun): need ddenseMatrix methods to avoid
397 :     infinite recursion in dispatch for some cases.
398 :    
399 : bates 2041 2007-08-02 08:48 Martin Maechler <maechler@stat.math.ethz.ch>
400 : maechler 2036
401 : bates 2041 * [r4693] src/chm_common.c: R_cholmod_printf() instead of Rprintf() just
402 :     so pointers match
403 :    
404 : maechler 2024 2007-08-02 Martin Maechler <maechler@stat.math.ethz.ch>
405 :    
406 : maechler 2036 * DESCRIPTION (Date): set ready for release -- 0.999375-1
407 : maechler 2024
408 : bates 2020 2007-08-01 15:44 Douglas Bates <bates@stat.wisc.edu>
409 :    
410 :     * [r4686] inst/include/Matrix.h, inst/include/Matrix_stubs.c,
411 :     src/chm_common.c, src/chm_common.h: Change API for
412 :     numeric_as_chm_dense and N_AS_CHM_DN
413 : maechler 2024
414 : maechler 2018 2007-08-01 Martin Maechler <maechler@stat.math.ethz.ch>
415 :    
416 :     * src/dtrMatrix.c (dtrMatrix_matrix_mm): fix dimensionality check (!)
417 :     * tests/matprod.R: regr.test for it
418 :    
419 : maechler 2011 2007-07-20 Martin Maechler <maechler@stat.math.ethz.ch>
420 :    
421 :     * R/dMatrix.R: fix from Brian for Math2(., digits = "missing")
422 :     * tests/group-methods.R: and regression-test it
423 :    
424 : bates 2008 2007-07-19 19:45 Douglas Bates <bates@stat.wisc.edu>
425 :    
426 :     * [r4642] inst/include/Matrix.h, inst/include/Matrix_stubs.c,
427 :     inst/include/cholmod.h, src/chm_common.c, src/init.c: Export
428 :     triplet_to_sparse, documentation, use typedefs
429 : maechler 2011
430 : maechler 2005 2007-07-18 Martin Maechler <maechler@stat.math.ethz.ch>
431 :    
432 :     * man/dpoMatrix-class.Rd: added 'corMatrix' example
433 :    
434 :     * src/dsyMatrix.[ch] (dsyMatrix_as_matrix): new 'keep_dimnames' arg
435 :     * src/dtrMatrix.[ch] (dtrMatrix_as_matrix): ditto
436 :     * src/init.c, R/dsyMatrix.R, R/dtrMatrix.R, R/lgTMatrix.R: ditto
437 :    
438 :     * R/lsparseMatrix.R: bug fix in "all" method
439 :     * R/Ops.R (.do.Logic.lsparse): "|" bug in borderline case
440 :    
441 :     * R/dsyMatrix.R (coerce->dsTMatrix): (i,j) slots should *not* have names
442 :     * R/ngTMatrix.R (coerce->ngTMatrix): ditto;
443 :     + matrix |-> nMatrix coercion
444 :     * R/pMatrix.R: + setAs() to dMatrix and from nMatrix
445 :     * man/pMatrix-class.Rd: ditto
446 :    
447 :     * R/Matrix.R (Summary): method for non-dMatrix
448 :    
449 :     * tests/Class+Meth.R (extraValid): new check about "dirty" slots
450 :     * tests/Class+Meth.R (tstMatrixClass): test norm(.);
451 :     test all Summary methods.
452 :    
453 :     2007-07-16 Martin Maechler <maechler@stat.math.ethz.ch>
454 :    
455 :     * R/dgeMatrix.R (norm, rcond): methods for 'matrix'
456 :    
457 :     2007-07-14 Martin Maechler <maechler@stat.math.ethz.ch>
458 :    
459 :     * R/sparseMatrix.R (norm): simple methods for sparseMatrix
460 :    
461 :     * R/pMatrix.R (t?crossprod): methods for pMatrix
462 :    
463 : bates 1987 2007-07-10 Douglas Bates <bates@stat.wisc.edu>
464 :    
465 :     * src/dgeMatrix.c (dgeMatrix_colsums): Get the logic straight.
466 :    
467 : bates 1975 2007-07-09 20:45 Douglas Bates <bates@stat.wisc.edu>
468 :    
469 :     * [r4579] src/dgeMatrix.c: Untangle horrible code in dgeMatrix_colsums
470 : maechler 2005 trying to fix a subtle bug - which has been somewhere else.
471 : bates 1975
472 :     2007-07-09 19:43 Martin Maechler <maechler@stat.math.ethz.ch>
473 :    
474 :     * [r4578] src/dgeMatrix.c: "cleaned" dgeMatrix_colsums() - but did not
475 :     solve the bug
476 :    
477 : maechler 1968 2007-07-08 Martin Maechler <maechler@stat.math.ethz.ch>
478 : bates 1964
479 : maechler 1968 * src/dgCMatrix.c (compressed_to_TMatrix):
480 :    
481 :     2007-07-07 Martin Maechler <maechler@stat.math.ethz.ch>
482 :    
483 :     * src/Csparse.c (Rsparse_validate): new, to have some validity
484 :     checking for RsparseMatrix
485 :     * src/dgCMatrix.c (xRMatrix_validate): ditto
486 :     * src/dtCMatrix.c (tRMatrix_validate): ditto
487 :    
488 :     2007-07-07 Douglas Bates <bates@stat.wisc.edu>
489 :    
490 : bates 1964 * [r4567] R/AllClass.R: Slots already in RsparseMatrix were redefined in
491 :     lgRMatrix
492 :     * [r4568] DESCRIPTION: Prepare for bug-fix release
493 : bates 1966 * [r4570] src/CHOLMOD/Check/cholmod_write.c: Include cholmod_matrixops.h
494 :     for declaration of cholmod_symmetry
495 : maechler 1968
496 : maechler 1961 2007-07-06 Martin Maechler <maechler@stat.math.ethz.ch>
497 :    
498 :     * DESCRIPTION (Version): 0.999375 merged into the trunk; ready for
499 :     release.
500 :    
501 : maechler 1960 2007-07-06 14:11 Douglas Bates <bates@stat.wisc.edu>
502 :    
503 :     * [r4559] src/iohb.c, src/iohb.h: Remove Harwell-Boeing input/output
504 :     functions - no longer used
505 :     * [r4560] src/HBMM.c, src/Mutils.c, src/dgTMatrix.c, src/dgeMatrix.c,
506 :     src/dspMatrix.c, src/dsyMatrix.c, src/dtCMatrix.c,
507 :     src/factorizations.c, src/sparseQR.c: Replace most calls to Calloc by
508 :     Alloca
509 :    
510 :     2007-07-06 13:14 Martin Maechler <maechler@stat.math.ethz.ch>
511 :    
512 :     * [r4558] inst/doc/Comparisons.Rnw, src/CHMfactor.c, src/Csparse.c,
513 :     src/Tsparse.c, src/chm_common.c, src/chm_common.h, src/dense.c,
514 :     src/dgCMatrix.c, src/dsCMatrix.c, src/dtTMatrix.c, src/sparseQR.c,
515 :     src/t_gCMatrix_colSums.c: more R_CheckStack()s
516 :    
517 :     2007-07-05 18:12 Douglas Bates <bates@stat.wisc.edu>
518 :    
519 :     * [r4550] inst/include/Matrix.h: Add the macro N_AS_CHM_DN to "alloca"
520 :     the required amount of memory then call M_numeric_as_chm_dense.
521 :     * [r4556] src/Mutils.h, src/dgCMatrix.c: Define and use the Alloca macro
522 :     (like Calloc but calling alloca)
523 :    
524 : maechler 1947 2007-07-05 Martin Maechler <maechler@stat.math.ethz.ch>
525 :    
526 :     * R/sparseMatrix.R (printSpMatrix): renamed from prSpMatrix()
527 :     and extended with more sophisticated 'col.names' option.
528 :     * NAMESPACE: export printSparseMatrix()
529 :     * man/printSpMatrix.Rd: document, incl. examples
530 :    
531 : maechler 1960 2007-07-04 16:21 Douglas Bates <bates@stat.wisc.edu>
532 :    
533 :     * [r4543] src/cs_utils.c, src/cs_utils.h, src/dgCMatrix.c,
534 :     src/dtCMatrix.c, src/sparseQR.c: CSP typedef for *cs and macro
535 :     AS_CSP. API change - pass the empty structure to Matrix_as_cs.
536 :    
537 : maechler 1945 2007-07-04 Martin Maechler <maechler@stat.math.ethz.ch>
538 :    
539 :     * DESCRIPTION (Version): 0.99875-4
540 :    
541 :     * tests/Class+Meth.R (tstMatrixClass): add dimnames, and hence test
542 :     some dimnames perservation.
543 :    
544 :     * R/dsTMatrix.R (t-method): keep dimnames
545 :     * R/dtTMatrix.R: ditto
546 :    
547 :     * R/sparseMatrix.R (prSpMatrix): print colnames when non-trivial
548 :     and ncol(.) < 10
549 :    
550 :     * src/cs_utils.c: drop check_class() and use Matrix_check_class()
551 :     from Mutils.h
552 :    
553 :     * src/lgCMatrix.c ([ln]csc_to_matrix): no longer lose dimnames,
554 :     e.g. in as(<ngCMatrix>, "matrix")
555 :    
556 : maechler 1960 2007-07-01 13:27 Douglas Bates <bates@stat.wisc.edu>
557 :    
558 :     * [r4529] .: Create a branch for the API changes from the 0.99875
559 :     series to the 0.999375 series
560 :     * [r4530] DESCRIPTION, inst/include/Matrix.h,
561 :     inst/include/Matrix_stubs.c, src/CHMfactor.c, src/Csparse.c,
562 :     src/Mutils.h, src/Tsparse.c, src/chm_common.c, src/chm_common.h,
563 :     src/dense.c, src/dgCMatrix.c, src/dsCMatrix.c, src/dtTMatrix.c,
564 :     src/t_gCMatrix_colSums.c: API change - pass the empty structure to the
565 :     as_cholmod_x functions
566 :    
567 :     2007-06-30 09:05 Martin Maechler <maechler@stat.math.ethz.ch>
568 :    
569 :     * [r4527] trunk/Matrix/DESCRIPTION, trunk/Matrix/NAMESPACE,
570 :     trunk/Matrix/inst/doc/Comparisons.Rnw: add session- and hardware-info
571 :     to Comparisons
572 :    
573 :     >>>>>>> .merge-right.r4561
574 : maechler 1932 2007-06-29 Martin Maechler <maechler@stat.math.ethz.ch>
575 :    
576 :     * DESCRIPTION (Version): 0.99875-3 ready to be released.
577 :    
578 :     * R/sparseMatrix.R (spMatrix): make spMatrix(3,4) working
579 :    
580 :     * R/AllGeneric.R: set "Math" (and "Math2") group generics in a way
581 :     that should also work in a future version of R.
582 :    
583 : maechler 1922 2007-06-21 Martin Maechler <maechler@stat.math.ethz.ch>
584 :    
585 :     * NAMESPACE, R/AllClass.R: "xsparseVector" class union.
586 :    
587 :     * R/sparseVector.R: more *sparseVector coercions, notably for
588 :     non - double ones.
589 :    
590 : maechler 1911 2007-06-19 Martin Maechler <maechler@stat.math.ethz.ch>
591 :    
592 :     * R/colSums.R: new file for all (col|row)(Sums|Means) methods,
593 :     notably the new ones building on the new .Call(.)s:
594 :    
595 :     * src/dgCMatrix.c (DEF_gCMatrix_COLSUMS): use to define
596 :     all 4 of [dlin]gCMatrix_colSums().
597 :    
598 : bates 1909 2007-06-18 16:12 Douglas Bates <bates@stat.wisc.edu>
599 :    
600 :     * [r4472] src/Syms.h, src/init.c: Added Matrix_lengthSym
601 :     * [r4473] src/dgCMatrix.c: Modified dgCMatrix_colSums for sparseVector
602 :     result
603 : maechler 1911
604 : maechler 1903 2007-06-16 Martin Maechler <maechler@stat.math.ethz.ch>
605 :    
606 : maechler 1904 * R/kronecker.R: fix typo (could lead to inf.recursion)
607 :     * test/simple.R: testing that
608 :    
609 : maechler 1903 * R/sparseMatrix.R (prSpMatrix): change to be used as print()
610 : maechler 1922 method as well (which can have arguments, show() can't).
611 : maechler 1903
612 : bates 1902 2007-06-16 15:52 Douglas Bates <bates@stat.wisc.edu>
613 :    
614 :     * [r4466] R/dgCMatrix.R, src/dgCMatrix.c, src/dgCMatrix.h, src/init.c:
615 :     added dgCMatrix_colSums for [col,row][Sums,Means]
616 :    
617 : bates 1899 2007-06-15 23:15 Douglas Bates <bates@stat.wisc.edu>
618 : bates 1897
619 :     * [r4460] R/sparseMatrix.R, man/dgCMatrix-class.Rd, src/dgCMatrix.c,
620 :     src/dgCMatrix.h, src/init.c: added lm.fit.sparse (unexported),
621 :     coercion of "factor" to "dgCMatrix" and dgCMatrix_cholsol
622 :     * [r4461] R/AllClass.R, man/sparseMatrix-class.Rd: draft "indicators"
623 :     class
624 : bates 1899 * [r4463] R/sparseMatrix.R, man/dgCMatrix-class.Rd,
625 :     man/sparseMatrix-class.Rd: Don't need an "indicators" class - use the
626 :     row names to store the levels - duh! Added an example.
627 : maechler 1903
628 : maechler 1893 2007-06-14 Martin Maechler <maechler@stat.math.ethz.ch>
629 :    
630 :     * src/Csparse.c (Csparse_validate): check for *repeated* entries
631 :     thanks to example from Christian Buchta; with a test here:
632 :     * tests/simple.R:
633 :    
634 : maechler 1886 2007-06-07 Martin Maechler <maechler@stat.math.ethz.ch>
635 :    
636 :     * R/Auxiliaries.R (callGeneric): another fix, needed for some cases
637 :     of colSums(*, sparseResult = TRUE)
638 :    
639 : maechler 1883 2007-06-06 Martin Maechler <maechler@stat.math.ethz.ch>
640 :    
641 :     * R/lsparseMatrix.R, R/ldenseMatrix.R (all, any): change default to
642 :     'na.rm = FALSE' as "everywhere" else in R.
643 :    
644 : bates 1877 2007-06-05 Douglas Bates <bates@stat.wisc.edu>
645 :    
646 : bates 1878 * [r4421] src/CSparse_install.sh: Modify for new organization of
647 : maechler 1883 CSparse package
648 : bates 1877 * [r4425] src/UFsparse_download.sh: Update to version 3.0.0 of
649 :     SuiteSparse
650 :     * [r4426] src/Makefile: add ./UFconfig to the include path for
651 :     compilation
652 : maechler 1883 * [r4427] src/cs.[ch]: update to CSparse version 2.2.0
653 :     * [r4428] inst/doc/UFsparse/* src/{AMD,CHOLMOD,COLAMD}/*
654 :     src/UFconfig/UFconfig.h: Update to version 3.0.0 of SuiteSparse
655 :    
656 : maechler 1870 2007-06-05 Martin Maechler <maechler@stat.math.ethz.ch>
657 :    
658 :     * R/Auxiliaries.R (emptyColnames): + argument msg.if.not.empty, used in
659 :     * R/sparseMatrix.R (prSpMatrix): now gives a message about
660 :     suppressed column names.
661 :    
662 : bates 1868 2007-06-04 17:13 Douglas Bates <bates@stat.wisc.edu>
663 :    
664 :     * [r4418] src/Csparse.c, src/HBMM.c, src/Mutils.c, src/Mutils.h,
665 :     src/Tsparse.c, src/chm_common.c, src/chm_common.h, src/dgCMatrix.c,
666 :     src/dgeMatrix.c, src/dpoMatrix.c, src/dpoMatrix.h, src/dppMatrix.c,
667 :     src/dppMatrix.h, src/dsCMatrix.c, src/dspMatrix.c, src/dspMatrix.h,
668 :     src/dsyMatrix.c, src/dsyMatrix.h, src/dtpMatrix.c, src/dtrMatrix.c:
669 :     Remove warnings after change to const char* CHAR
670 :    
671 :     2007-06-04 17:11 Douglas Bates <bates@stat.wisc.edu>
672 :    
673 :     * [r4417] inst/include/Matrix_stubs.c, inst/include/cholmod.h: Corrected
674 :     type of M_cholmod_ssmult
675 :    
676 : bates 1863 2007-06-03 14:42 Douglas Bates <bates@stat.wisc.edu>
677 :    
678 :     * [r4412] inst/include/Matrix_stubs.c, inst/include/cholmod.h,
679 :     src/init.c: Yet another cholmod export - cholmod_ssmult
680 :    
681 : maechler 1855 2007-05-23 Martin Maechler <maechler@stat.math.ethz.ch>
682 :    
683 :     * NAMESPACE: exported drop0(), since
684 :     * man/drop0.Rd: I have seen several cases, I really wanted to use
685 :     it, so our users may want too.
686 :    
687 :     2007-05-22 Martin Maechler <maechler@stat.math.ethz.ch>
688 :    
689 :     * man/colSums.Rd: separately document colSums() etc, since these
690 :     have the extra argument 'sparseResult'.
691 :    
692 : maechler 1852 2007-05-21 Martin Maechler <maechler@stat.math.ethz.ch>
693 :    
694 :     * R/sparseMatrix.R (spMatrix): utility (T)sparse Matrix constructor;
695 :     * man/spMatrix.Rd: docu., including examples
696 :    
697 :     * R/Auxiliaries.R (sp.colMeans): etc, using a patched callGeneric(),
698 :     in order to make colMeans() etc fast *and* correct.
699 :     * R/sparseVector.R (replSPvec): "[<-" functionality for
700 :     sparseVectors; tested in
701 :     * tests/simple.R:
702 :    
703 :     2007-05-19 Martin Maechler <maechler@stat.math.ethz.ch>
704 :    
705 :     * R/sparseMatrix.R (print.sparseSummary): and summary() method for
706 :     (very) sparse Matrices; output similar to Matlab's print().
707 :    
708 : bates 1847 2007-05-17 Douglas Bates <bates@stat.wisc.edu>
709 :    
710 :     * src/HBMM.c (Matrix_writeMatrixMarket): Write 1-based, not
711 :     0-based, indices (Jose Quesada <quesada@gmail.com>).
712 :    
713 : bates 1844 2007-05-16 Douglas Bates <bates@stat.wisc.edu>
714 :    
715 :     * R/CHMfactor.R: Added solve methods for a CHMfactor object.
716 :    
717 : maechler 1845 2007-05-16 Martin Maechler <maechler@stat.math.ethz.ch>
718 :    
719 :     * R/Auxiliaries.R (sparsapply): new utility, much faster than
720 :     tapply1() for large sparse matrices.
721 :    
722 :     2007-05-15 Martin Maechler <maechler@stat.math.ethz.ch>
723 :    
724 :     * R/Matrix.R (dim<-): reshape now via sparseVector.
725 :    
726 :     * R/sparseVector.R: methods and function for
727 :     * R/AllClass.R: new "sparseVector" class and daughters.
728 :     * NAMESPACE: export new classes
729 :    
730 : maechler 1837 2007-05-14 Martin Maechler <maechler@stat.math.ethz.ch>
731 :    
732 :     * DESCRIPTION (Version): 0.99875-1
733 :     * src/Makefile.win: also remove Lapack code from here (cf. 04-25).
734 :    
735 : maechler 1834 2007-05-11 Martin Maechler <maechler@stat.math.ethz.ch>
736 :    
737 :     * R/Tsparse.R ([, Tsparse): fix last case: *duplicated*, symmetric
738 :     indexing
739 :     * tests/indexing.R: test set for that.
740 :    
741 : maechler 1833 2007-05-08 Martin Maechler <maechler@stat.math.ethz.ch>
742 :    
743 :     * R/Tsparse.R (replTmat): fix the case of *duplicated* index
744 :     entries.
745 :     * tests/indexing.R(out): add regression test for it
746 :    
747 :     2007-04-30 Martin Maechler <maechler@stat.math.ethz.ch>
748 :    
749 :     * R/(l(dense|sparse))?Matrix.R (!): use 'x', not 'e1' as argument
750 :     name for "!" method definitions.
751 :    
752 : maechler 1829 2007-04-26 Martin Maechler <maechler@stat.math.ethz.ch>
753 :    
754 :     * R/Tsparse.R (intI): new utility, used for "[" :
755 :     Cleanup up there, and fixes for duplicated indices - more TODO!
756 :    
757 :     * tests/indexing.R(out): more tests
758 :    
759 : bates 1827 2007-04-25 Douglas Bates <bates@stat.wisc.edu>
760 :    
761 :     * DESCRIPTION,src/Makefile: require R>= 2.5.0 and remove Lapack
762 :     code that is now part of the R Lapack library.
763 : maechler 1829
764 : bates 1827 * src/init.c,inst/include/{Matrix_stubs.c,cholmod.h}:export
765 :     cholmod_factorize_p (used in lme4 for GLMMs and NLMMs).
766 :    
767 : maechler 1829 2007-04-21 Martin Maechler <maechler@stat.math.ethz.ch>
768 :    
769 :     * R/Matrix.R (image): method for all Matrices, not just sparse ones.
770 :    
771 :     2007-04-17 Martin Maechler <maechler@stat.math.ethz.ch>
772 :    
773 :     * R/Auxiliaries.R (tapply1): unname(.) -> colSums() etc don't end
774 :     up with extraneous names '0'...'<n-1>'
775 :    
776 : maechler 1825 2007-04-12 Martin Maechler <maechler@stat.math.ethz.ch>
777 :    
778 :     * R/dgTMatrix.R (mat2dgT): care about NAs
779 :    
780 :     2007-04-11 Martin Maechler <maechler@stat.math.ethz.ch>
781 :    
782 :     * R/kronecker.R: triangularity preserving methods
783 :    
784 : maechler 1803 2007-03-27 Martin Maechler <maechler@stat.math.ethz.ch>
785 :    
786 :     * R/kronecker.R: new file collecting kronecker() methods in one
787 :     place. Goal: become much faster!
788 :    
789 : maechler 1799 2007-03-23 Martin Maechler <maechler@stat.math.ethz.ch>
790 :    
791 :     * src/dtCMatrix.c (dtCMatrix_solve): use the new code from Kasper
792 :     Kristensen based cs_spsolve() instead of _lsolve & _usolve which
793 :     can be much faster.
794 :    
795 :     * tests/matprod.R: add regression tests for these (upper & lower).
796 :    
797 :     2007-03-19 Martin Maechler <maechler@stat.math.ethz.ch>
798 :    
799 :     * R/Matrix.R (diff): method for our Matrices.
800 :    
801 :     * R/sparseMatrix.R (isDiagonal): check dim()!
802 :    
803 :     2007-03-17 Martin Maechler <maechler@stat.math.ethz.ch>
804 :    
805 :     * R/Matrix.R (dim<-): new method for "reshape()" built on a
806 :     proposal from Tamas Papp.
807 :    
808 :     2007-03-16 Martin Maechler <maechler@stat.math.ethz.ch>
809 :    
810 :     * R/AllGeneric.R: remove all if(!isGeneric(.)) clauses
811 :    
812 :     * R/zzz.R (.onLoad, .onUnload): do *not* leave bind_activation(TRUE);
813 : maechler 1803 rather define and export cBind() and rBind() only.
814 :     --> useRs *must* change code that used to have cbind()/rbind() !!
815 : maechler 1799
816 : maechler 1803 * R/bind.R: change tests from cbind() to cBind() and similarly to rBind()
817 :     * R/bind.Rout.save: ditto
818 : maechler 1799
819 : bates 1787 2007-02-16 Douglas Bates <bates@r-project.org>
820 :    
821 :     * DESCRIPTION (Date, Version): 0.9975-11 with new date
822 :     * src/dgCMatrix.c (R_to_CMatrix, compressed_to_TMatrix): remove
823 :     const modifier on declaration of the array 'valid'
824 :    
825 : bates 1786 2007-02-12 Douglas Bates <bates@stat.wisc.edu>
826 :    
827 :     * R/CHMfactor.R: Add image method (coercion to sparseMatrix).
828 :    
829 : maechler 1765 2007-02-05 Martin Maechler <maechler@stat.math.ethz.ch>
830 :    
831 : maechler 1768 * DESCRIPTION (Date, Version): 0.9975-10 with new date.
832 :    
833 : maechler 1767 * R/Ops.R (Arith): make sure Csparse o Csparse also works for e.g. ntCMatrix
834 :     * tests/simple.R: test the above and some of these coercions:
835 :    
836 :     * R/nsparseMatrix.R: coercing "Csparse" to "lsparseMatrix";
837 :     be careful to avoid infinite recursion, using new coercions in
838 :     * R/ngCMatrix.R and nsC... and ntC...
839 :     * R/lsparseMatrix.R: ditto
840 :    
841 : maechler 1765 * R/SparseM-conv.R: more conversion, notably for triplet matrices.
842 :    
843 : maechler 1767 * src/dgCMatrix.c (R_to_C_Matrix): port Doug's fix and
844 :     * R/Rsparse.R: reactivate .Call()s
845 : maechler 1765
846 : maechler 1767 * tests/Class+Meth.R: a bit more on actual classes
847 :    
848 :     2007-02-04 Douglas Bates <bates@stat.wisc.edu>
849 :    
850 :     * src/dgCMatrix.c (compressed_to_TMatrix): fix memory bug using strdup()
851 :    
852 : maechler 1760 2007-02-03 Martin Maechler <maechler@stat.math.ethz.ch>
853 : maechler 1758
854 :     * DESCRIPTION (Version): 0.9975-10 to upload
855 :    
856 : maechler 1760 * tests/Class+Meth.R (tstMatrixClass): require coercions to
857 :     specific classes less unconditionally.
858 :    
859 :     * R/Auxiliaries.R: get rid of as_Tsparse() and as_Rsparse()
860 :    
861 :     * R/Tsparse.R (triu): etc, use as(*, "TsparseMatrix") instead of as_Tsparse()
862 :    
863 :     * R/Rsparse.R (.R.2.T): R-level workaround using compressed_to_TMatrix.
864 : maechler 1758 * R/Rsparse.R (.R.2.C): R-level workaround since C-level
865 :     R_to_CMatrix segfaults on one platform.
866 : maechler 1760 Eliminate most coercion method to *specific* classes, and replace
867 :     with virtual classes coercions.
868 : maechler 1758
869 : maechler 1760
870 : maechler 1758 2007-02-01 Martin Maechler <maechler@stat.math.ethz.ch>
871 :    
872 :     * src/init.c: export the CHM...._validate() placeholders, since
873 :     they *are* called.
874 :    
875 : maechler 1760 * tests/Class+Meth.R (classCanCoerce): and starting to test
876 : maechler 1758 all as(<from>, <to>)
877 :    
878 : maechler 1751 2007-01-30 Martin Maechler <maechler@stat.math.ethz.ch>
879 :    
880 :     * R/Tsparse.R ([): more care when subsetting triangular Tsparse
881 :     * tests/indexing.R: tested now
882 :     * tests/indexing.Rout.save: updated
883 :    
884 :     * src/Csparse.c (Csparse_to_dense): use Rkind = -1 for PATTERN to
885 :     * src/chm_common.c (chm_dense_to_SEXP): return "ngeMatrix" when
886 :     appropriate.
887 :    
888 :     * NAMESPACE: export a trivial
889 :     * R/Matrix.R: drop() Matrix-method
890 :    
891 :     * R/AllClass.R: moved all prototypes to virtual super classes.
892 :    
893 :     * R/Rsparse.R: many more coercions to have less exceptions in
894 :     * tests/Class+Meth.R:
895 :    
896 :     * R/Ops.R (Compare): tweak for case with NA
897 :     * tests/simpl.R: hence another 'FIXME' eliminated
898 :    
899 : maechler 1747 2007-01-29 Martin Maechler <maechler@stat.math.ethz.ch>
900 :    
901 : maechler 1748 * R/diagMatrix.R (solve): the obvious methods for diagonalMatrix
902 :     objects.
903 :    
904 : maechler 1747 * tests/Class+Meth.R (tstMatrixClass): now testing diag(), nnzero(),
905 :     and more of "!", "&", "|", all, any; coercions
906 :    
907 :     * R/Rsparse.R: many coercions (which enable quite a few other
908 :     methods), thanks to enhancements in
909 :     * src/dgCMatrix.c (R_to_CMatrix): new, and
910 :     * src/dgCMatrix.c (compressed_to_TMatrix): now for (d,l,n) ,
911 :     symmetric & triangular and ..RMatrix objects.
912 :    
913 :     * src/TMatrix_as.c (Matrix_T_as_DENSE,Matrix_T_as_GENERAL):
914 :     renamed file from src/dsTMatrix.c;
915 :     now dealing with symmetric and triangular Tsparse coercions, both
916 :     to dense and general.
917 :    
918 :     2007-01-27 Martin Maechler <maechler@stat.math.ethz.ch>
919 :    
920 :     * src/dsTMatrix.c: has now "l" and "n" methods besides the "d" ones.
921 :    
922 :     * R/Ops.R (Arith): <dgCMatrix> o <numeric> now remains sparse
923 :     where sensible when the <numeric> is of length > 1.
924 :    
925 :     2007-01-26 Martin Maechler <maechler@stat.math.ethz.ch>
926 :    
927 :     * R/Matrix.R ([<-): for M[] <- value: fix length
928 :    
929 :     2007-01-25 Martin Maechler <maechler@stat.math.ethz.ch>
930 :    
931 :     * R/Auxiliaries.R (n2l_Matrix): new, to be used in
932 :     * R/ndenseMatrix.R: new coercions n* -> l*
933 :    
934 : maechler 1738 2007-01-22 Martin Maechler <maechler@stat.math.ethz.ch>
935 :    
936 :     * R/triangularMatrix.R: new file; simple triu() and tril() methods.
937 :    
938 :     * R/Ops.R ("Logic"): and other "Ops", many updates
939 :    
940 :     2007-01-18 Martin Maechler <maechler@stat.math.ethz.ch>
941 :    
942 :     * src/Mutils.h (SET_DimNames): new utility
943 :    
944 :     * R/Auxiliaries.R (nnzero): improved and now exported via
945 :    
946 :     * NAMESPACE: + nnzero(); length() == prod(dim(.)) method for all "Matrix" objects
947 :    
948 : maechler 1725 2007-01-17 Martin Maechler <maechler@stat.math.ethz.ch>
949 :    
950 :     * R/diagMatrix.R (!): fix typo.
951 :    
952 :     2007-01-16 Martin Maechler <maechler@stat.math.ethz.ch>
953 :    
954 :     * R/Auxiliaries.R (as_Csparse): and quite a few others:
955 :     allow to pass class definition --> speedup
956 :     * R/sparseMatrix.R: apply the above
957 :    
958 :     * R/Csparse.R: coercion Csparse* to dense* now preserves shape properties.
959 :    
960 :     * src/Mutils.h (mMatrix_as_geMatrix): new, based on
961 :     * src/Mutils.c (dup_mMatrix_as_geMatrix): new; generalization of
962 :     old dup_mMatrix_as_dgeMatrix), eliminating a long-standing "FIXME".
963 :    
964 :     * src/dense.c (dense_to_Csparse): use new mMatrix_as_geMatrix()
965 :    
966 :     * R/denseMatrix.R (.dense2C): based on dense_to_Csparse: name it,
967 :     and use it for "sparse*" as well, since it's faster than the
968 :     as_Csparse(.) way.
969 :    
970 :     2007-01-15 Martin Maechler <maechler@stat.math.ethz.ch>
971 :    
972 :     * R/Ops.R ("Logic"): more methods, notably an <lgC> o <lgC> one.
973 :    
974 : maechler 1724 2007-01-12 Martin Maechler <maechler@stat.math.ethz.ch>
975 :    
976 :     * R/Tsparse.R (.TM.repl.i.2col): new internal function to be used
977 :     as method for M[ ij ] <- v
978 :     * R/Csparse.R:: go via Tsparse for "M[ij] <- v"
979 :    
980 :     * R/Ops.R: "Compare" for (C|R)sparse: need pointer slot for all
981 :     FALSE answer
982 :    
983 :     * R/Csparse.R (replCmat): fix the "all non-zero" case with reordering
984 :     * tests/indexing.R: test it, and some of the above
985 :    
986 :     2007-01-05 Martin Maechler <maechler@stat.math.ethz.ch>
987 :    
988 :     * R/Auxiliaries.R (is_duplicatedT): new utility
989 :    
990 : bates 1716 2007-01-05 Douglas Bates <bates@stat.wisc.edu>
991 :    
992 :     * src/init.c (R_init_Matrix): export cholmod_scale
993 :    
994 : maechler 1724 2006-12-30 Martin Maechler <maechler@stat.math.ethz.ch>
995 :    
996 :     * R/zzz.R (tmp): for R >= 2.5.0, extend formals of our
997 :     base::as.matrix to (x, ...)
998 :    
999 : maechler 1714 2006-12-28 Martin Maechler <maechler@stat.math.ethz.ch>
1000 :    
1001 :     * R/Ops.R ("Arith" etc): move almost all "Ops" methods to new R
1002 :     file; start using "Logic", hence
1003 :    
1004 :     * DESCRIPTION (Depends): R >= 2.4.1 (since we want "Logic")
1005 :     * NAMESPACE: import and export "Logic"
1006 :    
1007 :     2006-12-27 Martin Maechler <maechler@stat.math.ethz.ch>
1008 :    
1009 :     * src/zpotfr.f and dependencies: use LAPACK 3.1 version
1010 :     only needed previously to R version 2.5.0.
1011 : maechler 1724
1012 : maechler 1710 2006-12-26 Martin Maechler <maechler@stat.math.ethz.ch>
1013 :    
1014 :     * DESCRIPTION (Date, Version): 0.9975-8, ready for release
1015 :    
1016 :     * R/Tsparse.R (replTmat): fix subassignment of triangular
1017 :     * R/Csparse.R (replCmat): ditto
1018 :     * tests/indexing.R: more tests, incl the above fix
1019 :    
1020 :     2006-12-23 Martin Maechler <maechler@stat.math.ethz.ch>
1021 :    
1022 :     * R/Auxiliaries.R (drop0): extend for non CSparse
1023 :     * R/Auxiliaries.R (diagU2N): should work for all sparseMatrix
1024 :    
1025 :     * src/Csparse.c (Csparse_to_Tsparse, Csparse_general_to_symmetric):
1026 :     use uplo correctly (!); other places: use uplo_P() macro
1027 :    
1028 :     * R/Csparse.R (replCmat): call diagU2N() when needed
1029 :     * R/Tsparse.R (replTmat): ditto
1030 :    
1031 :     * src/dtCMatrix.c (tCMatrix_validate): new
1032 :     * src/dtTMatrix.c (tTMatrix_validate): new, used in
1033 :     * R/AllClass.R: for validity of dtC, dsC, and dtT, dsT.
1034 :    
1035 :     * R/diagMatrix.R (replDiag): to use in [<-
1036 :    
1037 : maechler 1708 2006-12-22 Martin Maechler <maechler@stat.math.ethz.ch>
1038 :    
1039 :     * R/Auxiliaries.R (as_Csparse2, as_geSimpl): new functions;
1040 :     also more general diagU2N().
1041 :    
1042 :     2006-12-21 Martin Maechler <maechler@stat.math.ethz.ch>
1043 :    
1044 :     * R/bind2.R: new file for all cbind2(), rbind() methods moved here
1045 :     from R/<foo>Matrix.R files. Better diagonal & improved sparse methods.
1046 :    
1047 : maechler 1707 2006-12-20 Martin Maechler <maechler@stat.math.ethz.ch>
1048 :    
1049 :     * tests/bind.R: a few more cases
1050 :     * R/Auxiliaries.R (.M.kind): also work for atomic vectors
1051 :    
1052 :     * R/denseMatrix.R (cbind2/rbind2): moved here (and generalized) from
1053 :     * R/ddenseMatrix.R (cbind2/rbind2)
1054 :     * R/Tsparse.R (replTmat): final(?!) fix for "[<-" ..
1055 :     * tests/indexing.R
1056 :     * tests/indexing.Rout.save: updated
1057 :    
1058 :     2006-12-18 Martin Maechler <maechler@stat.math.ethz.ch>
1059 :    
1060 :     * R/Tsparse.R (replTmat): fixed a remaining "[<-" bug in
1061 :     * tests/indexing.R
1062 :    
1063 : maechler 1705 2006-12-15 Martin Maechler <maechler@stat.math.ethz.ch>
1064 :    
1065 :     * R/sparseMatrix.R (prSpMatrix): "." alignment much improved:
1066 :     align with proper position of "0", i.e., right for integers.
1067 :     argument 'align' by default is "fancy".
1068 :    
1069 :     2006-12-14 Martin Maechler <maechler@stat.math.ethz.ch>
1070 :    
1071 :     * R/sparseMatrix.R: delegate "Compare" to "Csparse.."
1072 :     * R/Csparse.R: and fix "Compare" for more cases.
1073 :     * tests/Class+Meth.R: test some of these (m == m, m != m)
1074 :    
1075 :     2006-12-13 Martin Maechler <maechler@stat.math.ethz.ch>
1076 :    
1077 :     * R/lsparseMatrix.R: all() and any() methods
1078 :     * R/ldenseMatrix.R: ditto
1079 :     * NAMESPACE, R/Matrix.R: ditto
1080 :    
1081 :     * man/all-methods.Rd: document them minimally
1082 :    
1083 :     * tests/simple.R: add a few examples for these
1084 :    
1085 : maechler 1696 2006-12-11 Martin Maechler <maechler@stat.math.ethz.ch>
1086 :    
1087 :     * R/Tsparse.R ([): fix long standing typo in symmetric case
1088 :     * man/dsCMatrix-class.Rd: add example exhibiting the above case
1089 :    
1090 : bates 1691 2006-12-10 Douglas Bates <bates@stat.wisc.edu>
1091 :    
1092 :     * src/CHMfactor.c (CHMfactor_to_sparse): change LDL factorization
1093 :     to LL before converting to a sparse matrix. (The LDL form can be
1094 :     converted to a sparse matrix but it is implicitly a unit
1095 :     triangular matrix and a diagonal matrix overwritten on the diagonal.)
1096 :    
1097 :     2006-12-09 Douglas Bates <bates@stat.wisc.edu>
1098 :    
1099 :     * src/chm_common.c (chm_factor_to_SEXP): allocate and fill the Dim slot.
1100 :    
1101 : bates 1688 2006-12-08 Douglas Bates <bates@stat.wisc.edu>
1102 :    
1103 :     * DESCRIPTION (Version): updated -> release 0.9975-7
1104 :     * src/{init.c,chm_common.c}, inst/include/*: export cholmod_analyze_p
1105 :    
1106 : maechler 1682 2006-11-30 Martin Maechler <maechler@stat.math.ethz.ch>
1107 :    
1108 :     * R/diagMatrix.R (%*%): write a direct [diag o Csparse] method
1109 :    
1110 : bates 1681 2006-11-29 Douglas Bates <bates@stat.wisc.edu>
1111 :    
1112 :     * src/dgeMatrix.c (dgeMatrix_solve): Check error code from dgetri.
1113 :     * tests/dg_Matrix.R: Add Barry Rowlingson's test of a matrix that
1114 :     is exactly singular.
1115 :    
1116 : maechler 1674 2006-11-07 Martin Maechler <maechler@stat.math.ethz.ch>
1117 :    
1118 :     * DESCRIPTION (Date): updated -> release 0.9975-6
1119 :    
1120 : maechler 1673 2006-11-06 Martin Maechler <maechler@stat.math.ethz.ch>
1121 :    
1122 :     * R/Csparse.R (replCmat): symmetric indexing of symmetric matrix
1123 :     now returns symmetric.
1124 :    
1125 :     * R/zzz.R ("diag<-"): replace "diag<-" in base for R <= 2.4.x
1126 :    
1127 :     * R/Matrix.R (.M.sub.i.2col): new, for M[ cbind(i,j) ] indexing.
1128 :     * R/Matrix.R (.M.repl.i.2col): new, for M[ cbind(i,j) ] <- value
1129 :    
1130 :     * R/Auxiliaries.R (.type.kind): added
1131 :    
1132 :     2006-11-04 Martin Maechler <maechler@stat.math.ethz.ch>
1133 :    
1134 :     * src/cs.[ch]: updated to CSparse Version 2.0.3 by simply
1135 :     running src/CSparse_install.sh
1136 :    
1137 :     * R/denseMatrix.R: "[": keep symmetric on symmetric indexing.
1138 :    
1139 : maechler 1665 2006-11-03 Martin Maechler <maechler@stat.math.ethz.ch>
1140 :    
1141 :     * src/dsCMatrix.c (dsCMatrix_Csparse_solve): new
1142 :     * R/dsCMatrix.R (solve): "fully-sparse" using the above.
1143 :    
1144 :     * R/AllClass.R: "pMatrix" now also inherits from "generalMatrix"
1145 :    
1146 :     * tests/Class+Meth.R (tstMatrixClass): now assure
1147 :     the (important in method programming) property :
1148 :    
1149 :     ###>> Every "Matrix" is either
1150 :     ###>> "general*", "symmetric*", "triangular*" or "diagonal*"
1151 :    
1152 :     (where "*" stands for "Matrix")
1153 :    
1154 :     * R/Auxiliaries.R (diagU2N): now .Call()s Csparse_diagU2N for <Csparse>
1155 :    
1156 :     * R/dMatrix.R (Compare(<dMatrix>,<dMatrix>): update and
1157 :     * tests/validObj.R: checks for "comparison"
1158 :    
1159 :     * R/sparseMatrix.R ([): improved indexing for sparse;
1160 :     trying to keep <symmetric>[ n, n] symmmetric
1161 :    
1162 :     * tests/indexing.R: indexing for logical sparse now ok
1163 :    
1164 :    
1165 : maechler 1660 2006-11-02 Martin Maechler <maechler@stat.math.ethz.ch>
1166 :    
1167 : maechler 1661 * src/Tsparse.c: use xTsparse_validate() , and hence remove
1168 :    
1169 :     * src/{ltC,lsC,lgT}Matrix.[ch]: removed
1170 :    
1171 :     2006-11-02 Martin Maechler <maechler@stat.math.ethz.ch>
1172 :    
1173 : maechler 1660 * R/AllClass.R (Matrix-class): check length of dimnames in validity.
1174 :    
1175 :     * tests/simple.R: validObject() checking the above.
1176 :    
1177 : maechler 1665 * src/dgCMatrix.c (xCMatrix_validate): new, small and simple,
1178 : maechler 1660 replacing both dgCMatrix_validate and lgCM*.
1179 :    
1180 :     * src/Csparse.c (Csparse_dense_prod, etc): do not lose dimnames;
1181 :     fix dimnames setting in other places.
1182 :     * src/chm_common.c (chm_dense_to_SEXP): now can pass dimnames
1183 :    
1184 : maechler 1659 2006-11-01 Martin Maechler <maechler@stat.math.ethz.ch>
1185 :    
1186 : maechler 1660 * R/Csparse.R,src/Csparse.c, etc: tcrossprod(<CsparseM>,<CsparseM>)
1187 :    
1188 :     * R/sparseMatrix.R (isSymmetric): drop 'factors' slot for
1189 :     symmetry test, via
1190 : maechler 1659 * R/Auxiliaries.R (.as.dgC.0.factors):
1191 :    
1192 : bates 1657 2006-11-01 Douglas Bates <bates@r-project.org>
1193 :    
1194 :     * R/Csparse.R,src/Csparse.c,tests/matprod.R,
1195 :     man/CsparseMatrix-class.Rd: crossprod(<CsparseMatrix>,
1196 :     <CsparseMatrix>) added
1197 :    
1198 : maechler 1655 2006-10-30 Martin Maechler <maechler@stat.math.ethz.ch>
1199 :    
1200 :     * tests/matprod.R: add a variation of Harri's example
1201 :    
1202 :     * R/dsparseMatrix.R: fix crossprod(<dsparse>, <dge>) to *not*
1203 :     recursive infinitely.
1204 :    
1205 :     * R/dgCMatrix.R: + solve(<sparse>, <sparse>)
1206 :    
1207 :     * tests/indexing.R: add test for the "<" bug fixed 10-27 in R/dMatrix.R
1208 :    
1209 :     2006-10-28 Martin Maechler <maechler@stat.math.ethz.ch>
1210 :    
1211 :     * tests/Class+Meth.R (tstMatrixClass): more: use non-trivial
1212 :     matrix if possible; test m+m == 2*m; now test dgRMatrix.
1213 :     * R/dgRMatrix.R (.to.dgR): a few more coercions, in order to
1214 :     satisfy the above test.
1215 :    
1216 : maechler 1654 2006-10-27 Martin Maechler <maechler@stat.math.ethz.ch>
1217 :    
1218 : maechler 1655 * R/Matrix.R (Ops): <Matrix> o <matrix> method added
1219 :    
1220 : maechler 1654 * R/dgCMatrix.R: solve(a, b="missing") based on
1221 :     * src/dgCMatrix.c (dgCMatrix_matrix_solve): extend to work with
1222 :     RHS = NULL.
1223 :    
1224 :     * R/diagMatrix.R (diagdiagprod): extend %*% etc to ldiMatrix;
1225 :     add more (needed) [t]crossprod() methods.
1226 :    
1227 :     * man/ddiMatrix-class.Rd: more info, notably on 'diag'
1228 :    
1229 :     * R/Auxiliaries.R (as_CspClass): cleanup
1230 :     (drop0): internal utility for "Csparse_drop(*, 0)"
1231 :     (.bail.out.2): encourage active feedback
1232 :    
1233 :     2006-10-26 Martin Maechler <maechler@stat.math.ethz.ch>
1234 :    
1235 :     * R/dMatrix.R(Compare): new(), then slots [no validity check]
1236 :    
1237 :     * src/Csparse.c (Csparse_validate): fixed (and more efficient in
1238 :     non-valid or 'sorted' case).
1239 :    
1240 :     * R/dsparseMatrix.R: add "chol" method.
1241 :     * R/ddenseMatrix.R: ditto
1242 :    
1243 :     * R/diagMatrix.R (Ops): group methods for <diagonal> o <sparse>
1244 :     * NAMESPACE (Ops)
1245 :     * R/diagMatrix.R (diag2T): simple utility used "higher level"
1246 :     coercion; deprecating direct lower level coercions.
1247 :    
1248 :     * R/*.R (seq): use seq_len() and seq_along() where possible.
1249 :    
1250 :    
1251 : maechler 1647 2006-10-23 Martin Maechler <maechler@stat.math.ethz.ch>
1252 :    
1253 :     * DESCRIPTION (Version): 0.9975-5 ready for release
1254 :    
1255 : bates 1646 2006-10-20 Douglas Bates <bates@stat.wisc.edu>
1256 :    
1257 :     * src/init.c (R_init_Matrix): export more cholmod CCallable functions.
1258 :    
1259 : maechler 1642 2006-10-20 Martin Maechler <maechler@stat.math.ethz.ch>
1260 :    
1261 :     * R/AllClass.R (corMatrix): add 'validity' check;
1262 :     comment out unused "LDL" class definition
1263 :     * NAMESPACE: mention, but do not export "LDL" class
1264 :     * R/corMatrix.R: new (simple), needed for R-devel with
1265 :     * tests/Class+Meth.R (tstMatrixClass): 1 exception for corMatrix
1266 :     coerce and t() exceptions for all 5 'Mat.MatFact' classes.
1267 :    
1268 : bates 1641 2006-10-19 Douglas Bates <bates@stat.wisc.edu>
1269 :    
1270 :     * src/chm_common.h: Add R_cholmod_start to initialize cholmod to
1271 :     use Rprintf and R's error handling.
1272 :    
1273 : maechler 1635 2006-10-17 Martin Maechler <maechler@stat.math.ethz.ch>
1274 :    
1275 :     * R/diagMatrix.R (%*%): rep(*, each = .) in Matrix %*% diagonal.
1276 :     * tests/matprod.R: add tests for the bug fixed.
1277 :    
1278 : bates 1624 2006-10-11 Douglas Bates <bates@stat.wisc.edu>
1279 :    
1280 :     * src/HBMM.[ch]: remove HarwellBoeing format for writing.
1281 :     * src/SOURCES_C.mkf (SOURCES_C): no longer compile iohb.c
1282 :    
1283 :     2006-10-06 Douglas Bates <bates@stat.wisc.edu>
1284 :    
1285 : bates 1629 * R/d[gs]CMatrix.R: deprecate the writeHB function. Use writeMM instead.
1286 : bates 1624
1287 : maechler 1618 2006-10-06 Martin Maechler <maechler@stat.math.ethz.ch>
1288 :    
1289 :     * DESCRIPTION (Version): 0.9975-3
1290 :    
1291 :     * R/diagMatrix.R (bdiag): new function constructing block diagonal
1292 :     (sparse) matrices.
1293 :     * man/bdiag.Rd: docu + examples
1294 :    
1295 : maechler 1619 * R/Csparse.R (replCmat): calling new Csparse_drop() now.
1296 :    
1297 : maechler 1618 * src/Csparse.c (Csparse_general_to_symmetric, Csparse_drop): new functions
1298 :     * R/lsCMatrix.R: three more coercions to lsC (thanks to the above)
1299 :    
1300 :     * R/diagMatrix.R (Diagonal): '[<-' method for diag.matrices such
1301 :     that result is sparse or diagonal (and not dense).
1302 :    
1303 :     * man/Subassign-methods.Rd: fix examples
1304 :    
1305 :     * R/Matrix.R (Matrix): Matrix(0, *) or Matrix(*, sparse=TRUE)
1306 :     should always return a sparse (and not sometimes a diagonal) matrix.
1307 :    
1308 : maechler 1615 2006-10-05 Martin Maechler <maechler@stat.math.ethz.ch>
1309 :    
1310 :     * R/Matrix.R ([<-): also for value "Matrix" or "matrix"
1311 :    
1312 : bates 1613 2006-10-04 Douglas Bates <bates@stat.wisc.edu>
1313 :    
1314 :     * DESCRIPTION (Version): 0.9975-2
1315 : maechler 1615
1316 : bates 1613 * inst/include/Matrix_stubs.c (M_cholmod_sparse_to_triplet): export more symbols
1317 :    
1318 : bates 1611 2006-10-02 Douglas Bates <bates@R-project.org>
1319 :    
1320 :     * tests/dg_Matrix.R: Simplify test taking into account new code.
1321 :    
1322 : maechler 1599 2006-09-29 Martin Maechler <maechler@stat.math.ethz.ch>
1323 :    
1324 : maechler 1600 * R/Csparse.R (replCmat): improve for missing i / j in non-simple cases
1325 :    
1326 : maechler 1599 * R/lsTMatrix.R: new files w/ missing methods
1327 :     * R/nsTMatrix.R: " 'for completeness'
1328 :    
1329 :     * tests/Class+Meth.R: a bit less 'not.ok.classes'
1330 :    
1331 :     * R/Tsparse.R (t): generalized "t" method from "dgT*" to "Tsparse*"
1332 :    
1333 :    
1334 : bates 1595 2006-09-28 Douglas Bates <bates@R-project.org>
1335 :    
1336 :     * src/dppMatrix.h: Ensure definition of dspMatrix_validate is
1337 :     included.
1338 :    
1339 :     * src/init.c, inst/include/{Matrix.h,Matrix_stubs.h,cholmod.h}:
1340 :     Export C-callable functions used in Zt_create in lme4.
1341 :    
1342 : maechler 1592 2006-09-28 Martin Maechler <maechler@stat.math.ethz.ch>
1343 :    
1344 :     * DESCRIPTION (Version): 0.9975-1
1345 :    
1346 :     * tests/simple.R: less checks fail; using NA, found that our
1347 :     kronecker() is not base-compatible with NA's.
1348 :    
1349 :     * R/dMatrix.R: "Compare" method now implemented for all cases
1350 :    
1351 :     * R/Auxiliaries.R (indTri): == which([lower/upper].tri( * )) new utility
1352 :    
1353 :     * man/dtpMatrix-class.Rd: mention length of 'x' slot
1354 :    
1355 :     * src/dtpMatrix.c (dtpMatrix_validate): fix check
1356 :     * src/dspMatrix.c (dspMatrix_validate): ditto
1357 :    
1358 :     * R/dtTMatrix.R (gt2tT): fix ("l" -> "n")
1359 :     including coercion to [nl]tTMatrix.
1360 :    
1361 :     * R/diagMatrix.R (show): print a header line as for other classes.
1362 :    
1363 :     2006-09-27 Martin Maechler <maechler@stat.math.ethz.ch>
1364 :    
1365 :     * src/Makefile.win (SUBDIRS): fix typo
1366 :    
1367 : maechler 1583 2006-09-19 Martin Maechler <maechler@stat.math.ethz.ch>
1368 :    
1369 :     * DESCRIPTION (Date): ready to release 0.9975-0 to CRAN
1370 :    
1371 : bates 1577 2006-09-18 Douglas Bates <bates@stat.wisc.edu>
1372 :    
1373 :     * R/[CT]sparse.R (crossprod and tcrossprod): Handle the cases for x
1374 :     symmetric and y missing in R code using %*% (cholmod_aat doesn't
1375 :     accept a symmetric matrix).
1376 :     * tests/group-methods.R: Uncomment test of crossprod applied to
1377 :     lsCMatrix objects.
1378 :    
1379 : maechler 1575 2006-09-18 Martin Maechler <maechler@stat.math.ethz.ch>
1380 :    
1381 :     * R/AllClass.R (symmetricMatrix): add validity method (available
1382 :     in C for a long time). Many "n..Matrix": drop (wrong) validity arg.
1383 :    
1384 :     * src/lgCMatrix.c (lgCMatrix_validate): check 'x' slot (!)
1385 :    
1386 :     * tests/indexing.Rout.save:
1387 :     * tests/indexing.R: additions, mainly for 'lsparse'
1388 :    
1389 :     * R/diagMatrix.R (Diagonal) & coercion to lgTMatrix: fixes for NA
1390 :     case.
1391 :    
1392 :     * R/Auxiliaries.R (nz.NA): new utility now used in nnzero()
1393 :    
1394 : maechler 1571 2006-09-16 Martin Maechler <maechler@stat.math.ethz.ch>
1395 :    
1396 : maechler 1572 * R/sparseMatrix.R (prSpMatrix): print logical NAs "visibly"
1397 :     as 'N' (1-letter - Ok?)
1398 :    
1399 : maechler 1571 * tests/group-methods.R: add test for logical + NAs
1400 :    
1401 :     * R/dMatrix.R ("Compare"): fix to work with NA's
1402 :    
1403 :     * R/AllClass.R: "Cholesky" etc now inherit from MatrixFactorization.
1404 :    
1405 :     * src/lgCMatrix.c (ncsc_to_matrix): renamed from lcsc_to_matrix()
1406 :     which is implemented.
1407 :    
1408 : maechler 1565 2006-09-15 Martin Maechler <maechler@stat.math.ethz.ch>
1409 :    
1410 : maechler 1571 * src/chm_common.c: coerce logical <-> double instead of
1411 :     typecasting; needed for "l" matrix handling in cholmod.
1412 : maechler 1565
1413 : maechler 1571 * tests/other-pkgs.R (graph): small extension in "graph" checks.
1414 :    
1415 : maechler 1565 * R/sparseMatrix.R (graphNEL -> Tsparse): method for weight case.
1416 :     (Tsp2grNEL): other fixes needed
1417 :    
1418 : maechler 1548 2006-09-11 Martin Maechler <maechler@stat.math.ethz.ch>
1419 :    
1420 :     * R/AllClass.R ("nMatrix"): and subclasses for "nonzero pattern"
1421 :     Matrices, since "lMatrix", also "lsparseM" can have NA
1422 :     * R/ndenseMatrix.R, etc: new source files
1423 :     * man/nsparseMatrix-classes.Rd, etc: new help files
1424 :     * tests/: adaptions
1425 :     * src/chm_common.c (chm_dense_to_SEXP): and others:
1426 :     new 'Rkind' argument: "l*" and "d*" both use CHOLMOD_REAL
1427 : maechler 1582 * src/Csparse.c, etc: ditto
1428 : maechler 1548
1429 : bates 1546 2006-09-11 Douglas Bates <bates@R-project.org>
1430 :    
1431 :     * src/Mutils.[ch],init.c inst/include/*.h: Move the
1432 :     alloc_d**Matrix functions to the lme4 package.
1433 :    
1434 : bates 1543 2006-09-09 Douglas Bates <bates@R-project.org>
1435 :    
1436 :     * src/dsCMatrix.c (dsCMatrix_Cholesky): igoring LDL = FALSE now
1437 : maechler 1544 fixed
1438 : bates 1543
1439 : maechler 1544 2006-09-09 Martin Maechler <maechler@stat.math.ethz.ch>
1440 :    
1441 : maechler 1548 * R/lMatrix.R: new
1442 :    
1443 : maechler 1544 * R/sparseMatrix.R (Tsp2grNEL): do not yet use graph::foo()
1444 :    
1445 :     * R/dgeMatrix.R: do not define tcrossprod() methods for "matrix"
1446 : maechler 1582 * man/tcrossprod.Rd: ditto
1447 : maechler 1544
1448 : bates 1538 2006-09-08 Douglas Bates <bates@stat.wisc.edu>
1449 :    
1450 :     * inst/include/Matrix_stubs.c,Matrix.h: Add declarations and stubs
1451 :     for exported functions
1452 :     * src/Makefile, src/CHOLMOD/Lib/Makefile, src/Metis,CAMD,CCOLAMD:
1453 :     Remove partitioning algorithms for sparse matrix reordering. The
1454 :     copyright on the Metis code was problematic and the methods were
1455 :     rarely used.
1456 :     * src/triplet_to_col.[ch],MMHB.[ch]: Remove triplet_to_col. Such
1457 :     operations are now done entirely in CHOLMOD code.
1458 :    
1459 : bates 1517 2006-09-06 Douglas Bates <bates@R-project.org>
1460 :    
1461 :     * src/Mutils.h: Remove functions that are no longer used.
1462 :    
1463 : bates 1507 2006-09-04 Douglas Bates <bates@R-project.org>
1464 :    
1465 :     * src/dtCMatrix.c (dtCMatrix_validate): rename functions.
1466 :     * src/DEPS.mkf: update
1467 :    
1468 : maechler 1481 2006-09-02 Martin Maechler <maechler@stat.math.ethz.ch>
1469 :    
1470 :     * created branches/Matrix-for-R-2.3.x; on trunk: do
1471 :     * DESCRIPTION (Version): 0.9975-0
1472 :     (Depends): R (>= 2.4.0)
1473 :    
1474 : bates 1475 2006-09-01 Douglas Bates <bates@R-project.org>
1475 :    
1476 :     * R/sparseMatrix.R: Added direct method to CsparseMatrix from graphNEL
1477 :    
1478 : maechler 1472 2006-09-01 Martin Maechler <maechler@stat.math.ethz.ch>
1479 :    
1480 :     * R/sparseMatrix.R: add coercion from "ANY" to "sparseMatrix"
1481 :     * R/denseMatrix.R: add coercion from "ANY" to "denseMatrix"
1482 :    
1483 :     * R/Matrix.R ([): use nargs() to disambiguate M[i] and M[i,]
1484 :    
1485 :     2006-08-31 Martin Maechler <maechler@stat.math.ethz.ch>
1486 :    
1487 :     * R/sparseMatrix.R (Arith): moved Arith group method one-level up
1488 :     from "dsparse" to "sparse" and now go via "Csparse" instead of "dgC"
1489 : maechler 1582 * R/dsparseMatrix.R: ditto
1490 :     * R/Csparse.R: ditto
1491 : maechler 1472
1492 :     2006-08-31 Martin Maechler <maechler@stat.math.ethz.ch>
1493 :    
1494 :     * R/dMatrix.R (Compare): improve availability of "<", etc
1495 :     * R/Auxiliaries.R (asTuniq): new; also make use of R 2.4.x print(*,max)
1496 :    
1497 : maechler 1467 2006-08-30 Martin Maechler <maechler@stat.math.ethz.ch>
1498 :    
1499 :     * R/dgCMatrix.R: aargh: "Arith(<dgC>, numeric)" was wrong because
1500 :     of a 0-index which was used as 1-index (..hmm)
1501 :    
1502 :     * R/sparseMatrix.R (prSpMatrix): fix printing an all-0 sparse Matrix
1503 :    
1504 :     * R/Auxiliaries.R (all0, is0): for 0-testing in presence of NA's
1505 :     * R/Auxiliaries.R (isTriMat): use all0() for 0-testing.
1506 : maechler 1582 (.is.diagonal): ditto
1507 : maechler 1467
1508 :     * R/lgTMatrix.R: as("matrix", "lgTMatrix"): warn about NA's
1509 :    
1510 :     * R/Matrix.R (Matrix): also work for NA data
1511 :    
1512 : maechler 1455 2006-08-28 Martin Maechler <maechler@stat.math.ethz.ch>
1513 :    
1514 :     * R/Matrix.R (Matrix): + 'forceCheck' argument; dimnames setting
1515 :     in all cases.
1516 :    
1517 : bates 1453 2006-08-27 Douglas Bates <bates@R-project.org>
1518 :    
1519 :     * src/dense.[ch],init.c, R/ddenseMatrix.R, man/band.Rd
1520 :     (ddense_band): Added triu, tril and band for ddenseMatrix objects.
1521 :    
1522 : maechler 1447 2006-08-25 Martin Maechler <maechler@stat.math.ethz.ch>
1523 :    
1524 :     * src/Mutils.c (dup_mMatrix_as_dgeMatrix): added all subclasses of
1525 :     subclasses of "ddenseMatrix"
1526 :     * src/init.c et al: outcomment dtrM*_as_dge* and dsyM*_as_dge*_
1527 :     * R/ddenseMatrix.R et al: setAs("ddenseMatrix", "dgeMatrix", ..)
1528 :     instead of half dozen specialized ones.
1529 :    
1530 : bates 1445 2006-08-25 Douglas Bates <bates@R-project.org>
1531 :    
1532 :     * R/lmer.R (qqmath method): Bug fix provided by Emmanuel Tillard
1533 :     <tillard@cirad.fr> - ordering standard errors to match effects.
1534 :    
1535 : bates 1439 2006-08-24 Douglas Bates <bates@R-project.org>
1536 : bates 1431
1537 : bates 1439 * src/lsCMatrix.c (lsCMatrix_trans): Remove lsCMatrix_chol based
1538 :     on R_ldl.
1539 :     * R/lCholCMatrix.R,
1540 :     src/[dl]CholCMatrix.[ch],R_ldl.[ch],Metis_utils.[ch]: removed
1541 :     * src/dsCMatrix.c (dsCMatrix_to_dgTMatrix): use CHOLMOD
1542 :     * many files in ./R and ./src: Use more general version of
1543 :     dup_mMatrix_as_dgeMatrix to simplify method definitions.
1544 : bates 1442 * src/Mutils.c (dup_mMatrix_as_dgeMatrix): Add ddiMatrix,
1545 :     dtpMatrix, dspMatrix and dppMatrix conversions.
1546 :    
1547 : maechler 1447
1548 : bates 1439 2006-08-23 Douglas Bates <bates@R-project.org>
1549 :    
1550 :     * R/AllClass.R,lCholCMatrix.R,src/SOURCES_C.mkf,init.c,NAMESPACE:
1551 :     Remove classes lCholCMatrix and dCholCMatrix based on R_ldl code.
1552 : bates 1431 * src/dgeMatrix.c: Ensure 'factors' slot exists in result of
1553 :     dgeMatrix_crossprod (may need to do this in other places).
1554 :     * R/AllGeneric.R,dsCMatrix.R, src/dscMatrix.[ch]: Add Cholesky
1555 :     generic and method for dsCMatrix. Use CHOLMOD for chol().
1556 :    
1557 : bates 1414 2006-08-22 Douglas Bates <bates@R-project.org>
1558 :    
1559 :     * src/Mutils.c (dup_mMatrix_as_dgeMatrix): updated for general
1560 :     types of classed Matrices, matrices or numeric or logical vectors.
1561 : bates 1423 * src/init.c: register dup_mMatrix_as_dgeMatrix for coercions.
1562 :     * src/chm_common.c,Mutils.h (as_cholmod_factor): Move check_class
1563 :     to Mutils.h (as an inline) and change name to Matrix_check_class;
1564 :     fixes in as_cholmod_factor and chm_factor_to_SEXP.
1565 :     * src/dsCMatrix.[ch]: Use CHOLMOD for dsCMatrix_chol and
1566 :     dsCMatrix_matrix_solve. Comment out vestigial functions.
1567 :     * src/Csparse.c: use diag_P and uplo_P macros.
1568 : maechler 1447
1569 : bates 1405 2006-08-21 Douglas Bates <bates@R-project.org>
1570 :    
1571 :     * src/lmer.c (internal_mer_RZXinv): Fix memory leak caught by
1572 : maechler 1447 valgrind.
1573 : bates 1411 * tests/matprod.R: Add tests to verify that 'solve' and '%*%' are
1574 :     inverses.
1575 :     * src/sparseQR.c (sparseQR_validate): add new validation test, fix
1576 :     -Wall warnings.
1577 :     * src/dppMatrix.c,dtrMatrix.c,dgCMatrix.c,dgeMatrix.c,dspMatrix.c:
1578 :     Use dup_mMatrix_as_dgeMatrix.
1579 : maechler 1447
1580 : bates 1403 2006-08-20 Douglas Bates <bates@R-project.org>
1581 :    
1582 :     * src/sparseQR.c: Fix thinko in sparseQR_resid_fitted.
1583 :     * tests/sparseQR.R: Added
1584 :     * man/sparseQR-class.Rd: Document methods for qr.* generics
1585 :     * R/sparseQR.R: Return correct # of coefs; fix cut-and-paste errors
1586 :    
1587 : bates 1398 2006-08-19 Douglas Bates <bates@R-project.org>
1588 :    
1589 :     * NAMESPACE, R/sparseQR.R, src/init.c,sparseQR.[ch],SOURCES_C.mkf:
1590 :     Added methods for sparseQR for qr.qy, qr.qty, qr.coef, qr.resid
1591 :     and qr.fitted.
1592 :     * src/Mutils.[ch]: Added dup_mMatrix_as_dgeMatrix utility
1593 :     * src/dgCMatrix.c: Check for ordering before storing q in dgCMatrix_QR
1594 :    
1595 : maechler 1389 2006-08-18 Martin Maechler <maechler@stat.math.ethz.ch>
1596 :    
1597 :     * R/AllGeneric.R: add "qr" and "chol" generics; via 'trick' since
1598 :     the base version has no "..." argument.
1599 :    
1600 :     * R/sparseMatrix.R (prSpMatrix): fix the triangular unit diagonal case.
1601 :    
1602 :     * R/Matrix.R: define and
1603 :     * NAMESPACE: export as.numeric() and as.logical() methods.
1604 :     Let's hope these do not badly slow down something...
1605 :     Finally export the zapsmall() method.
1606 :    
1607 : bates 1388 2006-08-17 Douglas Bates <bates@R-project.org>
1608 :    
1609 :     * src/dgCMatrix.[ch] (dgCMatrix_matrix_solve), src/init.c,
1610 :     R/dgCMatrix.R: solve methods for dgCMatrix and dense RHS.
1611 :     * src/dtCMatrix.c :Remove code that is no longer used
1612 :     * R/dtCMatrix.R: Use C code for diagU2N in CsparseMatrix classes
1613 :    
1614 : bates 1370 2006-08-14 Douglas Bates <bates@R-project.org>
1615 :    
1616 : bates 1373 * src/Csparse.[ch],init.c (Csparse_to_logical): Added utilities
1617 :     Csparse_to_logical and Csparse_symmetric_to_general.
1618 :     * R/dgCMatrix.R,dsCMatrix.R,Csparse.R : Consolidate general
1619 : maechler 1389 coercion methods between CsparseMatrix and TsparseMatrix.
1620 : bates 1373
1621 :     2006-08-14 Douglas Bates <bates@R-project.org>
1622 :    
1623 : bates 1370 * R/dtCMatrix.R,dgCMatrix.R,Csparse.R src/init.c,dgCMatrix.[ch],
1624 :     Csparse.[ch],chm_common.c,dense.c : Use CHOLMOD code and methods
1625 :     for CsparseMatrix, TsparseMatrix, denseMatrix or matrix when
1626 :     possible.
1627 :    
1628 : bates 1368 2006-08-12 Douglas Bates <bates@R-project.org>
1629 :    
1630 :     * src/chm_common.[ch],Csparse.[ch],Tsparse.[ch],CHMfactor.c,dtTMatrix.c,
1631 :     dgTMatrix.c,dgCMatrix.c,dsCMatrix.c,dtTMatrix.c, R/dsTMatrix.R,
1632 :     Tsparse.R,Csparse.R,dgTMatrix.R,dsCMatrix.R,lsCMatrix.R:
1633 :     generalize conversions between TsparseMatrix, CsparseMatrix,
1634 :     denseMatrix and matrix. Preserve triangularity property and
1635 :     propagate Dimnames in the easy cases.
1636 :    
1637 : bates 1365 2006-08-10 Douglas Bates <bates@R-project.org>
1638 :    
1639 :     * src/lmer.c: adjust checks in glmer_init for S4SXP
1640 :     * tests/validObj.R: check of all(eq) should be all(eq@x) - worked
1641 :     before S4SXP but for the wrong reasons.
1642 :    
1643 : bates 1354 2006-08-08 Douglas Bates <bates@R-project.org>
1644 :    
1645 : bates 1360 * src/Csparse.c (Csparse_crossprod): tcrossprod result has stype = -1.
1646 :     Later modified to return the upper triangle only.
1647 :     * R/dgTMatrix.R: Remove vestigial crossprod and tcrossprod methods.
1648 : maechler 1389
1649 : bates 1352 2006-08-07 Douglas Bates <bates@R-project.org>
1650 :    
1651 :     * src/Csparse.c (Csparse_crossprod): Set stype on result to avoid
1652 :     R-level conversion to a sparse symmetric class.
1653 :     * R/Tsparse.R,R/Csparse.R (crossprod and tcrossprod methods):
1654 :     Remove conversion to sparse symmetric classes (now done in C code).
1655 :    
1656 : maechler 1349 2006-08-07 Martin Maechler <maechler@stat.math.ethz.ch>
1657 :    
1658 : maechler 1351 * R/dgCMatrix.R: disable old crossprod and tcrossprod methods
1659 :     * man/band.Rd: adapt the \dontshow{} unit test.
1660 :    
1661 :     2006-08-07 Martin Maechler <maechler@stat.math.ethz.ch>
1662 :    
1663 : maechler 1349 * DESCRIPTION (Version): 0.995-14 for CRAN
1664 :    
1665 :     * tests/other-pkgs.R: oops: library(Matrix) outside *if* !
1666 :    
1667 :     * R/sparseMatrix.R (Tsp2grNEL): fixed Tsparse -> graph coercion
1668 :     * tests/other-pkgs.R: more checks, sparseMatrix -> graph
1669 :    
1670 :     * R/Auxiliaries.R (as_Tsparse, as_Rsparse): new
1671 :     * R/Tsparse.R (tril, triu, band): methods
1672 : bates 1352 * R/dgRMatrix.R (tril, ...): ditto
1673 :     * man/band.Rd: ditto
1674 : maechler 1349
1675 :     2006-08-04 Martin Maechler <maechler@stat.math.ethz.ch>
1676 :    
1677 :     * R/Matrix.R (head, tail): directly use utils:::head.matrix
1678 :     to be up-to-date automatically.
1679 :    
1680 : maechler 1346 2006-08-03 Martin Maechler <maechler@stat.math.ethz.ch>
1681 :    
1682 :     * DESCRIPTION (Version): 0.995-13 to be released to CRAN
1683 :    
1684 :     * DESCRIPTION (Lazydata): no, instead of 'yes' because it fails for:
1685 :     * data/CAex.R, inst/external/CAex_slots.rda: replacing data/CAex.rda
1686 :     * data/KNex.R, inst/external/KNex_slots.rda: replacing data/KNex.rda
1687 :     such that the S4 objects are always created by the current version
1688 :     of R and 'Matrix' class definitions.
1689 :    
1690 : bates 1342 2006-08-01 Douglas Bates <bates@R-project.org>
1691 :    
1692 :     * R/lmer.R (LMEoptimize method), tests/lmer.R,
1693 : maechler 1346 inst/external/test3comp.rda: Added warnings for convergence on
1694 : bates 1342 boundary and test cases.
1695 :    
1696 :     * src/lmer.c (mer_postVar): Modified to return the variances that
1697 :     are marginal to the fixed effects, not conditional on them (which
1698 :     is what the bVar slot contents represent).
1699 :    
1700 : bates 1338 2006-07-31 Douglas Bates <bates@R-project.org>
1701 :    
1702 :     * NAMESPACE, src/lmer.c, R/lmer.R (hatTrace): Add the hatTrace
1703 :     function which calls the C function mer_hat_trace2.
1704 : maechler 1346
1705 : bates 1342 * man/ranef.Rd: Include description of "postVar" argument and
1706 :     producing a caterpillar plot.
1707 : bates 1338
1708 : maechler 1335 2006-07-31 Martin Maechler <maechler@stat.math.ethz.ch>
1709 :    
1710 :     * NAMESPACE: change "correlation" to "corMatrix"
1711 :     * R/AllClass.R: to avoid clash with S3 class in 'nlme'.
1712 : bates 1352 * R/dpoMatrix.R: ditto
1713 :     * R/lmer.R: ditto
1714 : maechler 1335
1715 : bates 1338 2006-07-28 Douglas Bates <bates@R-project.org>
1716 :    
1717 :     * src/lmer.c (internal_mer_RZXinv): Split the calculation of the
1718 :     RZXinv slot's contents into a separate internal function that can
1719 :     be used in mer_hat_trace.
1720 :    
1721 : maechler 1331 2006-07-22 Martin Maechler <maechler@stat.math.ethz.ch>
1722 :    
1723 :     * R/Matrix.R: Coercions "Matrix" -> (sparse|dense)Matrix
1724 :     via new smart
1725 :     * R/Auxiliaries.R (as_Csparse, as_dense, .M.shapse): new
1726 :     utility functions.
1727 :    
1728 :    
1729 : maechler 1330 2006-07-21 Martin Maechler <maechler@stat.math.ethz.ch>
1730 :    
1731 : maechler 1331 * R/Csparse.R (tril, triu, band): do return *triangular* classed
1732 :     matrices when appropriate; band() even symmetric ones.
1733 :     (replCmat): extend to potentially all "CsparseMatrix"
1734 :     * R/Tsparse.R (replTmat): extend to all "TsparseMatrix"; hence
1735 :     allow subassignment for special sparse matrices.
1736 :    
1737 :     * R/Auxiliaries.R (as_geClass): factor out the .M.kind() functionality
1738 :    
1739 : maechler 1330 * src/lmer.c (mer_MCMCsamp, glmer_MCMCsamp): new 'verbose'
1740 :     argument; in glmer_*(): print only if(verbose).
1741 :    
1742 :     speed-optimize a few places by moving REAL(.) out of loops.
1743 :    
1744 :     * src/lmer.h, src/init.h, R/lmer.R: related to above.
1745 :    
1746 : maechler 1329 2006-07-20 Martin Maechler <maechler@stat.math.ethz.ch>
1747 :    
1748 :     * R/Matrix.R("["): disable ("Matrix", i = "logical", j = "missing"),
1749 :     since that wrongly triggers also for M[ logi , ]
1750 :    
1751 :     * R/denseMatrix.R: "[" methods now also work e.g. when indexing
1752 :     a symmetric matrix that results in a non-symmetric one.
1753 :     * R/Auxiliaries.R (as_geClass): new function used in "[" above.
1754 :    
1755 :     * R/dMatrix.R: make round(M) work as round(M, 0)
1756 :    
1757 :     * R/dgTMatrix.R (image): coordinate system and axis now use
1758 :     1-based indices, not 0-based ones.
1759 :    
1760 :     * R/Tsparse.R (.ind.prep for "["): get rid of max(<empty>) warning.
1761 :     * tests/indexing.R: test it.
1762 :    
1763 :     * NAMESPACE: export isSymmetric(); has been a generic in "base" for a while;
1764 :     * man/isSymmetric-methods.Rd: and document it.
1765 :    
1766 :     * R/SparseM-conv.R: added coercion methods for some 'SparseM' matrices.
1767 :     * man/SparseM-conv.Rd: docu them
1768 :    
1769 :     * tests/other-pkgs.R: renamed from tests/graph.R and add example
1770 :     for 'SparseM' conversions
1771 :    
1772 :     2006-07-17 Douglas Bates <Douglas.Bates@R-project.org>
1773 :    
1774 :     * R/Matrix.R (head): added head() and tail() methods.
1775 :    
1776 :     2006-07-17 Martin Maechler <maechler@stat.math.ethz.ch>
1777 :    
1778 :     * DESCRIPTION (Version): 0.995-12 released to CRAN
1779 :    
1780 : maechler 1319 2006-07-15 Martin Maechler <maechler@stat.math.ethz.ch>
1781 :    
1782 :     * tests/simple.R: add check for correct dsT -> dgT coercion;
1783 :     add check for correct printing of symmetric sparse matrices.
1784 :    
1785 :     * R/Auxiliaries.R (non0ind): return *all* non-0 entry indices also
1786 :     for sparse symmetric matrices.
1787 :    
1788 :     * src/dsTMatrix.c (dsTMatrix_as_dgTMatrix): do not copy the
1789 :     diagonal twice.
1790 :    
1791 : bates 1316 2006-07-11 Douglas Bates <Douglas.Bates@R-project.org>
1792 :    
1793 :     * src/dsTMatrix.c (dsTMatrix_as_dgTMatrix): Fix a case of INTEGER
1794 : maechler 1319 being applied to the x slot (detected by Brian Ripley).
1795 : bates 1316
1796 : maechler 1315 2006-07-10 Martin Maechler <maechler@stat.math.ethz.ch>
1797 :    
1798 :     * src/dgCMatrix.c (dgCMatrix_validate): 'p' slot must have correct length.
1799 :    
1800 :     * R/Auxiliaries.R (isTriC): fix buglet (we were 1-based!)
1801 :    
1802 :     2006-07-08 Martin Maechler <maechler@stat.math.ethz.ch>
1803 :    
1804 :     * src/lgCMatrix.c (lgCMatrix_diag): new function
1805 :     * R/lgCMatrix.R (diag): for new method
1806 :    
1807 :     * R/AllClass.R (TsparseMatrix): do use Tsparse_validate
1808 :     ==> construction of illegal "*gTMatrix" via new() should
1809 :     now be much less easy:
1810 :     * tests/Class+Meth.R: assertError() for some illegal "dgT*"
1811 :    
1812 :     * R/Matrix.R (Matrix): Matrix(0, nrow,ncol) now "goes sparse"
1813 :     directly.
1814 :     * man/Matrix.Rd: documents it.
1815 :    
1816 : bates 1311 2006-07-06 Douglas Bates <bates@R-project.org>
1817 :    
1818 :     * src/pedigree.c (pedigree_inbreeding): Correction in
1819 :     initialization. This function is not currently being used and is
1820 :     not fully tested.
1821 :    
1822 : bates 1312 * NAMESPACE, R/{AllClass.R,lmer.R}, src/{init.c,lmer.c}:
1823 :     Introduced the glmer class. Added code for mcmcmsamp on glmer
1824 :     objects. Modified validity check on pedigree objects to account
1825 :     for nonparallel patterns of missingness of parents.
1826 : bates 1311
1827 : bates 1313 * man/{lmer-class.Rd,mcmcsamp.Rd}: Update documentation for glmer
1828 :     class.
1829 : maechler 1315
1830 :     2006-07-01 Martin Maechler <maechler@stat.math.ethz.ch>
1831 :    
1832 :     * R/pMatrix.R: coercion pMatrix -> Tsparse
1833 :    
1834 : bates 1300 2006-06-12 Douglas Bates <bates@R-project.org>
1835 :    
1836 : maechler 1319 * DESCRIPTION (Version): 0.995-11 released to CRAN
1837 :    
1838 : bates 1300 * R/lmer.R (mcmcsamp method): Corrected arrangments of names on
1839 :     the output from mcmcsamp.
1840 :    
1841 : bates 1298 2006-06-10 Douglas Bates <bates@R-project.org>
1842 :    
1843 : bates 1300 * R/lmer.R (simulestimate): added C code for calculating the trace
1844 :     of the hat matrix.
1845 : bates 1298
1846 : maechler 1295 2006-06-09 Martin Maechler <maechler@stat.math.ethz.ch>
1847 :    
1848 :     * R/diagMatrix.R (setAs): define coercion methods to sparse matrix
1849 :     classes.
1850 : maechler 1315 * R/sparseMatrix.R etc: multiplication of diagonal and sparse
1851 : maechler 1295
1852 : maechler 1290 2006-06-08 Martin Maechler <maechler@stat.math.ethz.ch>
1853 :    
1854 :     * R/dgTMatrix.R (colSums): etc. All four of
1855 :     colSums(), rowSums(), colMeans(), rowMeans() now should work for
1856 :     all "Matrices".
1857 :    
1858 : bates 1288 2006-06-01 Douglas Bates <bates@stat.wisc.edu>
1859 :    
1860 :     * R/lmer.R (panel.ci): Add a reference line at zero and a
1861 :     background grid to the qqmath plot of ranef.lmer.
1862 :    
1863 : bates 1287 2006-05-30 Douglas Bates <bates@stat.wisc.edu>
1864 : bates 1284
1865 : bates 1287 * R/lmer.R (expandSlash): Functions (non-exported) to allow nested
1866 :     grouping factors to be specified in the formula as (1|foo/bar).
1867 :    
1868 :     2006-05-27 Douglas Bates <bates@stat.wisc.edu>
1869 :    
1870 : bates 1284 * R/lmer.R (findbars and others): Change check of is.numeric to
1871 :     !is.language to resolve the bug reported by Jacob Wegelin.
1872 :    
1873 :     * src/pedigree.c (pedigree_inbreeding): Initial implementation of
1874 :     code to evaluate inbreeding coefficients without calculating T,
1875 :     based on code in Sargolzaei and Iwaisaki's paper.
1876 :    
1877 : bates 1283 2006-05-27 Douglas Bates <bates@stat.wisc.edu>
1878 :    
1879 :     * R/{lmer.R,AllGeneric.R}, src/{init.c,lmer.[ch]}: Added local
1880 :     generic and mer methods for isNested and denomDF. This denomDF was
1881 :     an attempt to emulate that in lme but I don't think that makes
1882 :     sense. Use the trace of the hat matrix instead.
1883 :    
1884 : maechler 1271 2006-05-17 Martin Maechler <maechler@stat.math.ethz.ch>
1885 :    
1886 :     * R/sparseMatrix.R: Matrix <-> graph methods: can no longer use
1887 :     the C code depending on a slot structure that's no longer valid.
1888 : bates 1352 * src/dgTMatrix.c: ditto (also: src/init.c src/dgTMatrix.h)
1889 : maechler 1271
1890 :    
1891 : bates 1268 2006-05-17 Douglas Bates <bates@stat.wisc.edu>
1892 :    
1893 :     * R/{AllGeneric.R,Csparse.R},man/band.Rd,NAMESPACE: changed name
1894 :     of lowerTriMatrix generic and methods to tril (also upper to triu)
1895 :     and added a general band extractor.
1896 :    
1897 : bates 1267 2006-05-16 Douglas Bates <bates@stat.wisc.edu>
1898 :    
1899 :     * R/pedigree.R (pedigree): Replace sire and dam values outside the
1900 :     allowable range with NAs. Added a corresponding check in the
1901 :     validity check for the pedigree class.
1902 :    
1903 :     * R/[CT]sparse.R ([t]crossprod): The result of single-argument
1904 :     crossprod methods now inherits from symmetricMatrix.
1905 :    
1906 : bates 1265 2006-05-15 Douglas Bates <bates@stat.wisc.edu>
1907 :    
1908 :     * R/AllGeneric.R (lowerTriMatrix): Added (but did not export)
1909 :     generics lowerTriMatrix and upperTriMatrix along with methods for
1910 :     the Csparse virtual class. Also added a C function Csparse_band
1911 :     that implements these methods by calling cholmod_band.
1912 :    
1913 : maechler 1264 2006-05-15 Martin Maechler <maechler@stat.math.ethz.ch>
1914 :    
1915 :     * R/Tsparse.R ("["): column or row subsetting; @Dimnames[k] got
1916 :     erased when it was NULL. This led to invalid subselections!
1917 :    
1918 : bates 1259 2006-04-25 Douglas Bates <bates@stat.wisc.edu>
1919 :    
1920 :     * R/dtCMatrix.R: avoid coercion of dtCMatrix object to dgCMatrix
1921 :     in method for "t" so as not to lose the unit diagonal property.
1922 :    
1923 : bates 1257 2006-04-19 Douglas Bates <bates@stat.wisc.edu>
1924 :    
1925 :     * R/lmer.R, R/AllGeneric.R, NAMESPACE: Remove the postVar generic
1926 :     and methods. This is now an option to the ranef method for the
1927 :     mer class.
1928 :    
1929 :     * src/cs_utils.c: Ensure that the nz component is -1 for a
1930 :     compressed column-oriented matrix. Minor formatting cleanup.
1931 :    
1932 :     * man/lmer-class.Rd: Document the qqmath method for ranef.lmer
1933 :     objects.
1934 :    
1935 : maechler 1253 2006-04-19 Martin Maechler <maechler@stat.math.ethz.ch>
1936 :    
1937 :     * R/Auxiliaries.R (diagU2N): new for the solve() methods in
1938 :     * R/dtCMatrix.R: where dgC -> dgT coercion now preserves diag = "U".
1939 :    
1940 : bates 1251 2006-04-15 Douglas Bates <bates@stat.wisc.edu>
1941 :    
1942 :     * src/cs.[ch],src/cs_utils.[ch] : Added Tim Davis' CSparse library
1943 :     in cs.[ch] and utilities to interface to that code in cs_utils.[ch].
1944 :    
1945 :     * R/dtCMatrix.R, src/dtCMatrix.[ch] : CSparse-based solve methods
1946 :     for the dtCMatrix class.
1947 : maechler 1253
1948 : bates 1247 2006-04-12 Douglas Bates <bates@stat.wisc.edu>
1949 :    
1950 :     * R/pedigree.R, R/AllClass.R, NAMESPACE: added a pedigree class
1951 :     and methods for it.
1952 :    
1953 : maechler 1245 2006-04-12 Martin Maechler <maechler@stat.math.ethz.ch>
1954 :    
1955 :     * R/dgCMatrix.R: add storage.mode(.) <- "double" for "matrix"
1956 :     arguments, such that M %*% 1:6 now works
1957 :     * Tests/matprod.R: test the above
1958 :    
1959 : bates 1244 2006-04-03 Douglas Bates <bates@stat.wisc.edu>
1960 : bates 1243
1961 :     * R/lmer.R (qqmath,ranef.lmer-method): added a qqmath method for
1962 :     the ranef.lmer class.
1963 :    
1964 :     * R/AllClass.R, NAMESPACE, R/lmer.R: Added a postVar generic and
1965 :     methods to extract the posterior variances from the bVar slot.
1966 :    
1967 : maechler 1238 2006-03-30 Martin Maechler <maechler@stat.math.ethz.ch>
1968 :    
1969 :     * R/dtCMatrix.R: allow coercion from dgC* to triangular (dtC*)
1970 :     * R/dsCMatrix.R: and symmetric (dsC*) 'Csparse' matrices.
1971 :    
1972 :     * R/Tsparse.R: Tsparse* -> Csparse* coercion now works and is tested in
1973 :     * tests/simple: (extended)
1974 :    
1975 :     * R/sparseMatrix.R (isTriangular): now using much improved
1976 :     * R/Auxiliaries.R (isTriC): new triangularity check for *CMatrix
1977 :    
1978 : bates 1236 2006-03-23 Douglas Bates <bates@stat.wisc.edu>
1979 :    
1980 :     * src/dsyMatrix.c (dsyMatrix_as_dspMatrix): Propagate DimNames
1981 :     (problem report from Franklin Parlamis). This should be done
1982 : maechler 1238 generally.
1983 : bates 1236
1984 : bates 1234 2006-03-21 Douglas Bates <bates@stat.wisc.edu>
1985 :    
1986 :     * R/AllClass.R,lmer.R: Change the name of the lmer.ranef class to
1987 :     ranef.lmer (like summary.lmer). Add the coef.lmer class and
1988 :     update the plot methods.
1989 :    
1990 : bates 1232 2006-03-20 Douglas Bates <bates@stat.wisc.edu>
1991 :    
1992 :     * R/lmer.R (resid and ranef methods): Added methods for the
1993 :     "residuals" and "resid" generic but only for linear mixed model
1994 :     fits. Changed the ranef method to return a list of data frames so
1995 :     that the plot methods now work.
1996 :    
1997 : bates 1230 2006-03-16 Douglas Bates <bates@bates2>
1998 :    
1999 :     * src/dpoMatrix.c (dpoMatrix_chol): Require n > 0 in call to
2000 :     dpotrf - otherwise the BLAS on Mac OS X complains and quits.
2001 :    
2002 :     * DESCRIPTION (Date): New release
2003 :    
2004 : maechler 1228 2006-03-15 Martin Maechler <maechler@stat.math.ethz.ch>
2005 :    
2006 :     * DESCRIPTION (Version): 0.995-6 -- to be released to CRAN
2007 :    
2008 :     * data/KNex.rda: replacing 'mm' and 'y' by KNex <- list(mm=mm, y=y)
2009 :     * man/KNex.Rd: and other help files
2010 :     * tests/*.R: several ones needed adaption
2011 : bates 1352 * inst/doc/Comparisons.Rnw: ditto
2012 : maechler 1228
2013 : maechler 1226 2006-03-11 Martin Maechler <maechler@stat.math.ethz.ch>
2014 :    
2015 :     * R/dgCMatrix.R (replCmat): "[<-" methods for dgCMatrix
2016 :    
2017 :     * tests/indexing.R: tests for new [<- methods for sparse matrices.
2018 :    
2019 :     2006-03-10 Martin Maechler <maechler@stat.math.ethz.ch>
2020 :    
2021 :     * R/dgTMatrix.R (replTmat): "[<-" methods for dgTMatrix
2022 :    
2023 :     * R/Tsparse.R (.ind.prep): fix out-of-range indexing
2024 :    
2025 :     2006-03-08 Martin Maechler <maechler@stat.math.ethz.ch>
2026 :    
2027 :     * R/dMatrix.R: enable things like M [ M < 10 ]
2028 :     * R/dgeMatrix.R: implement it
2029 :    
2030 : maechler 1222 2006-03-06 Martin Maechler <maechler@stat.math.ethz.ch>
2031 :    
2032 :     * R/AllClass.R: define "summary.mer" and "*.lmer"
2033 :     * R/lmer.R (summary): summary(<mer>) computes & returns the above;
2034 :     * R/lmer.R (show): now works with summary()
2035 :    
2036 :     2006-03-04 Martin Maechler <maechler@stat.math.ethz.ch>
2037 :    
2038 :     * R/dgCMatrix.R: finally direct "Arith" dgC o dgC
2039 :     * R/Auxiliaries.R (WhichintersectInd): and other utilities to
2040 :     support the above
2041 :    
2042 : bates 1213 2006-02-07 Douglas Bates <bates@stat.wisc.edu>
2043 :    
2044 :     * R/lmer.R (lmer): fix initial values of offset and weights for glm.fit.
2045 :     Use glmFit$prior.weights for weights in a glmm.
2046 :     Allow an option usePQL = FALSE to skip the PQL steps for the
2047 :     Laplace method (and, in time, the AGQ method).
2048 :    
2049 :     * src/lmer.c (mer_factor): Move downdating and factoring of XtX
2050 :     into a separate function internal_mer_Xfactor to be able to call
2051 :     it from internal_bhat.
2052 :    
2053 : maechler 1200 2006-01-23 Martin Maechler <maechler@stat.math.ethz.ch>
2054 :    
2055 :     * tests/Class+Meth.R (tstMatrixClass): function for much better
2056 :     testing; now again of all actual classes.
2057 :    
2058 :     * src/Mutils.c (MAKE_TRIANGULAR_BODY, MAKE_SYMMETRIC_BODY):
2059 :     use macros and define make_d_matrix_* and make_i_matrix_*
2060 :     where _i_ is for the ldense routines:
2061 :    
2062 :     * src/ldense.c (ltrMatrix_as_lgeMatrix): provide functions
2063 :     * src/ldense.c (lsyMatrix_as_lgeMatrix):
2064 :    
2065 :     * R/ldenseMatrix.R: use the above in setAs(*,"lgeMatrix")
2066 :    
2067 :    
2068 : maechler 1174 2006-01-16 Martin Maechler <maechler@stat.math.ethz.ch>
2069 :    
2070 :     * R/Matrix.R (Matrix): has become much "smarter" now auto-producing
2071 :     many different kinds of matrices.
2072 :     * R/*.R: quite a few new methods were needed for R CMD check with
2073 :     new Matrix(). Very good for users playing around.
2074 :    
2075 :    
2076 : maechler 1165 2006-01-15 Martin Maechler <maechler@stat.math.ethz.ch>
2077 :    
2078 :     * src/dgeMatrix.c (dMatrix_validate): new
2079 :     * src/Mutils.c (dense_nonpacked_validate): new
2080 :    
2081 :     * src/dtrMatrix.c (dtrMatrix_validate): improved/fixed
2082 :    
2083 :    
2084 :     2006-01-14 Douglas Bates <bates@stat.wisc.edu>
2085 :    
2086 :     * R/AllClass.R (compMatrix), (generalMatrix): new virtual classes
2087 :    
2088 : bates 1123 2006-01-07 Douglas Bates <bates@stat.wisc.edu>
2089 : bates 1119
2090 : maechler 1127 * DESCRIPTION (Version): 0.99-6 released to CRAN
2091 :    
2092 : bates 1119 * src/dgBCMatrix.c (cscb_trcbsm): Fix due to Peter Dalgaard for
2093 :     segfault in cases with multiple non-nested grouping factors.
2094 :    
2095 : maechler 1109 2006-01-03 Martin Maechler <maechler@stat.math.ethz.ch>
2096 :    
2097 :     * DESCRIPTION (Version): 0.99-4 to be released to CRAN
2098 :     (Depends): also on 'utils'
2099 :    
2100 :     * R/AllClass.R (diagonalMatrix): new class with "ddi*" and "ldi*"
2101 :     * R/diagMatrix.R (Diagonal): constructor and methods for
2102 :     diagonal matrices
2103 :    
2104 :     * R/ltTMatrix.R: new "minimal methods"
2105 :    
2106 : maechler 1091 2005-12-12 Martin Maechler <maechler@stat.math.ethz.ch>
2107 :    
2108 :     * R/AllGeneric.R (tcrossprod): 2-argument version; here, and for
2109 :     all methods (and help files).
2110 :    
2111 : maechler 1084 2005-12-09 Martin Maechler <maechler@stat.math.ethz.ch>
2112 :    
2113 :     * R/Auxiliaries.R (dimNamesCheck): fixed thinko -> bug
2114 :     for case (dimn. op no_dimn.)
2115 :    
2116 :     2005-11-14 Douglas Bates <bates@stat.wisc.edu>
2117 :    
2118 : maechler 1174 * DESCRIPTION (Version): 0.99-2 released to CRAN
2119 : maechler 1084
2120 : bates 988 2005-10-21 Douglas Bates <bates@stat.wisc.edu>
2121 :    
2122 :     * R/lmer.R (simulate method): Fixed a drop=FALSE problem reported
2123 :     by Julian Faraway.
2124 :    
2125 : maechler 976 2005-10-06 Martin Maechler <maechler@stat.math.ethz.ch>
2126 :    
2127 :     * R/Auxiliaries.R (try_as): new utility
2128 :     * R/sparseMatrix.R: use try_as() in coercion to original class
2129 :    
2130 : maechler 956 2005-09-30 Martin Maechler <maechler@stat.math.ethz.ch>
2131 :    
2132 :     * src/dgCMatrix.c (double_to_csc): and dgeMatrix_to_csc()
2133 :    
2134 :     2005-09-29 Martin Maechler <maechler@stat.math.ethz.ch>
2135 :    
2136 :     * R/Auxiliaries.R (dimNamesCheck): added
2137 :    
2138 :     * R/Matrix.R (as.array), (as.vector): new
2139 :    
2140 : maechler 954 2005-09-28 Martin Maechler <maechler@stat.math.ethz.ch>
2141 :    
2142 :     * R/Matrix.R (Matrix): get logical argument 'sparse' with a smart
2143 : maechler 956 default.
2144 :     * R/AllClass.R: move 'factors' slot toplevel "Matrix";
2145 :     "pMatrix" now contains "sparseMatrix"
2146 : maechler 954
2147 : maechler 948 2005-09-26 Martin Maechler <maechler@stat.math.ethz.ch>
2148 :    
2149 :     * tests/Class+Meth.R: new tests; t(t(m)) == m
2150 :    
2151 :     * src/dtCMatrix.c (tsc_transpose): add forgotten "diag" slot
2152 :    
2153 :     * src/dsTMatrix.c (dsTMatrix_as_dsCMatrix): bad typo (segfault!)
2154 :     * src/dtTMatrix.c (dtTMatrix_as_dtCMatrix): new
2155 :    
2156 :     * R/dspMatrix.R: typo in "t" method
2157 :    
2158 : maechler 925 2005-09-18 Douglas Bates <bates@wisc.edu>
2159 :    
2160 :     * R/AllClass.R (TsparseMatrix), CsparseM* and RsparseM*
2161 :     * R/Tsparse.R: instead of R/gTMatrix.R
2162 :     * R/Csparse.R: new
2163 :     * src/Tsparse.c (Tsparse_to_Csparse): new; -> cholmod_()
2164 :     * src/Tsparse.c: new; many trivial methods calling cholmod_()
2165 :     * src/Csparse.c (Csparse_to_Tsparse), transpose, (mat|cross)prod:
2166 :     via cholmod
2167 :    
2168 :     2005-09-16 Martin Maechler <maechler@stat.math.ethz.ch>
2169 :    
2170 :     * R/Auxiliaries.R (non0ind): new function using new C code
2171 :     * src/dgCMatrix.c (compressed_non_0_ij): new utility
2172 :    
2173 : bates 917 2005-09-15 Douglas Bates <bates@localhost.localdomain>
2174 :    
2175 :     * src/chm_common.h: header file required by all C sources that
2176 : maechler 1174 call CHOLMOD functions. It defines a cholmod_common structure
2177 : bates 917 called 'c' whose address is passed as the last argument to
2178 :     (virtually) every CHOLMOD function.
2179 :    
2180 :     * src/Pattern.c: Simple example of the use of CHOLMOD.
2181 :    
2182 :     * src/init.c: initialize and finalize the cholmod_common structure.
2183 :    
2184 :     * src/Makefile: Added source packages CHOLMOD UMFPACK AMD COLAMD
2185 :     LDL and CCOLAMD from the U. of Florida sparse matrix library.
2186 :    
2187 : maechler 908 2005-09-08 Martin Maechler <maechler@stat.math.ethz.ch>
2188 :    
2189 :     * inst/test-tools.R: new file collecting the utility functions used
2190 :     in ./tests/*.R
2191 :    
2192 :     * R/ddenseMatrix.R (cbind2): new methods for "numeric" and "matrix"
2193 :     * R/Matrix.R (cbind2): methods for NULL and missing
2194 :    
2195 : maechler 886 2005-08-31 Martin Maechler <maechler@stat.math.ethz.ch>
2196 :    
2197 :     * R/AllClass.R: new "index" class for "[" and "[<-":
2198 :     First cut at "symmetricMatrix" and "triangularMatrix"
2199 :     * R/gTMatrix.R (.ind.prep): new function;
2200 : maechler 1174 Logical and character indexing now work too.
2201 : maechler 886 * R/Matrix.R: cheap "[<-" methods for denseMatrix now work
2202 :     * tests/indexing.R: new, including *.Rout.save
2203 :     * tests/dgTMatrix.R: new
2204 :    
2205 : bates 876 2005-08-29 Douglas Bates <bates@wisc.edu>
2206 :    
2207 :     * src/dgTMatrix.c (graphNEL_as_dgTMatrix): Corrected the position
2208 :     indicator pos not being updated. Also enforced upper triangular
2209 :     for symmetric case. Need to coerce edges component of elements of
2210 :     edge list - grr! (Why don't they define their classes cleanly?)
2211 :    
2212 : maechler 871 2005-08-26 Martin Maechler <maechler@stat.math.ethz.ch>
2213 :    
2214 :     * R/Matrix.R: added first "[<-" methods; not yet functional
2215 : bates 1352 * R/denseMatrix.R: ditto
2216 : maechler 871 * man/Subassign-methods.Rd: new help file for these
2217 :    
2218 :     2005-08-25 Martin Maechler <maechler@stat.math.ethz.ch>
2219 :    
2220 :     * DESCRIPTION (Version): 0.98-6
2221 :    
2222 :     * R/denseMatrix.R: new file for "[" fallback methods for all dense
2223 :     matrices.
2224 :    
2225 : maechler 868 2005-08-19 Martin Maechler <maechler@stat.math.ethz.ch>
2226 :    
2227 :     * src/lgCMatrix.c (lcsc_to_matrix): new; need for
2228 :     as( <logical>, "matrix")
2229 :    
2230 :     * R/pMatrix.R: coercion to "lgTMatrix"
2231 :    
2232 :     * R/gTMatrix.R: new virtual class to define "[" methods for.
2233 :     * man/gTMatrix-class.Rd:
2234 :     * General slight re-organization of where "[" methods are defined.
2235 :     more to come.
2236 :    
2237 : maechler 871 2005-08-18 Douglas Bates <bates@wisc.edu>
2238 : maechler 868
2239 : maechler 1174 * DESCRIPTION (Version): 0.98-5 released to CRAN
2240 : maechler 871
2241 :     * src/dgTMatrix.c (graphNEL_as_dgTMatrix): add first graphNEL methods
2242 :     * .....
2243 :    
2244 : bates 863 2005-08-18 Douglas Bates <bates@localhost.localdomain>
2245 :    
2246 :     * R/lmer.R: Corrected naming scheme in mcmcsamp to work with lmer
2247 :     or glmer objects.
2248 :    
2249 : maechler 860 2005-08-17 Martin Maechler <maechler@stat.math.ethz.ch>
2250 :    
2251 :     * DESCRIPTION (Version): 0.98-4 : upload to CRAN
2252 :    
2253 :     2005-08-16 Douglas Bates <bates@localhost.localdomain>
2254 :    
2255 :     * R/HBMM.R: finish re-writing R-only code.
2256 :    
2257 : bates 854 2005-08-15 Douglas Bates <bates@localhost.localdomain>
2258 :    
2259 :     * man/externalFormats.Rd: move documentation for writeHB and
2260 :     writeMM here.
2261 :    
2262 :     * src/mmio.c: replace inclusion of <malloc.h> by <stdlib.h>
2263 :     (suggested by Paul Roecker).
2264 :    
2265 :     * tests/validObj.R (assertError): Comment out test that is failing
2266 :     after recent changes in r-devel.
2267 :    
2268 : maechler 860
2269 : maechler 848 2005-08-11 Martin Maechler <maechler@stat.math.ethz.ch>
2270 :    
2271 :     * R/AllClass.R: intermediate virtual class "denseMatrix"
2272 :     * man/denseMatrix-class.Rd
2273 :     * NAMESPACE: export it, and also export
2274 :     * man/unused-classes.Rd: "iMatrix", "zMatrix" and "ldenseMatrix"
2275 :    
2276 : bates 846 2005-08-10 Douglas Bates <bates@wisc.edu>
2277 :    
2278 : maechler 848 * DESCRIPTION (Version): 0.98-3 to CRAN
2279 :    
2280 : bates 846 * src/dtrMatrix.c (dtrMatrix_validate): fixed up validation and
2281 :     matrix_solve code (which was really, really wrong).
2282 :    
2283 : bates 835 2005-08-07 Douglas Bates <bates@wisc.edu>
2284 : maechler 834
2285 :     * DESCRIPTION (Version): 0.98-2
2286 :    
2287 :     * R/HBMM.R (readHB), (readMM): read Matrix Market formats
2288 :    
2289 :     * R/lmer.R (abbrvNms): new
2290 :     * R/lmer.R (mcmcsamp): allow transformed parameters
2291 : bates 835 * src/HBMM.c (Matrix_writeMatrixMarket): Added read/write routines
2292 :     for the Harwell-Boeing and the MatrixMarket formats.
2293 : maechler 834
2294 :     2005-08-04 Martin Maechler <maechler@stat.math.ethz.ch>
2295 :    
2296 :     * man/dtrMatrix-class.Rd: add examples
2297 : bates 835 * man/dtpMatrix-class.Rd: ditto; plus note about PROBLEM
2298 : maechler 834
2299 :     * TODO: note the dtpMatrix (docu) bug
2300 :    
2301 :     * R/zzz.R (.onLoad): assignInNamespace("as.matrix", *, "base")
2302 :     in order to ensure that new as.matrix() is used by old functions,
2303 :     e.g., svd(), qr(), eigen(), dist(),..;
2304 :     apply(), also matplot() or pairs().
2305 :    
2306 :    
2307 :     2005-08-03 Martin Maechler <maechler@stat.math.ethz.ch>
2308 :    
2309 :     * R/lmer.R: add 'fixme' comments and move the linear vs glm check;
2310 :     add comments about 'control' / lmerControl() arguments
2311 :    
2312 : bates 835 2005-07-27 Douglas Bates <bates@wisc.edu>
2313 : bates 820
2314 : bates 835 * man/sleepstudy.Rd: Added the sleep data set.
2315 : maechler 1174 * DESCRIPTION (Version): 0.98-1 released to CRAN
2316 : bates 820
2317 : bates 835 2005-07-12 Douglas Bates <bates@wisc.edu>
2318 : maechler 834 * man/sleepstudy.Rd: Added the sleep data set.
2319 :    
2320 : bates 809 * R/lmer.R (glmmMCMC): Added PACKAGE = "Matrix" in a couple of
2321 :     .Call calls that were producing spurious output.
2322 :    
2323 : bates 835 2005-07-05 Douglas Bates <bates@wisc.edu>
2324 : bates 801
2325 :     * R/lmer.R (lmer): stored updated variance component estimates in
2326 :     mer object for the generalized model. (Bug reported by Renaud
2327 :     Lancelot).
2328 :    
2329 : bates 835 2005-07-03 Douglas Bates <bates@wisc.edu>
2330 : bates 794
2331 :     * src/lmer.c (glmer_devAGQ): Added AGQ for single grouping factor,
2332 :     unidimensional case.
2333 :    
2334 : bates 835 2005-06-08 Douglas Bates <bates@wisc.edu>
2335 : maechler 791
2336 :     * DESCRIPTION (Version): 0.96-1
2337 :    
2338 : maechler 1174 * moved lmer-class' R and C code moved from lme4 to here
2339 : maechler 791
2340 : bates 835 2005-06-04 Douglas Bates <bates@wisc.edu>
2341 : bates 763
2342 :     * R/dgCMatrix.R: Call to csc_matrix_mm used undefined arguments
2343 :     (reported by Guissepe Ragusa <gragusa@ucsd.edu>)
2344 :    
2345 : bates 835 2005-06-02 Douglas Bates <bates@wisc.edu>
2346 : bates 763
2347 :     * src/Makefile.win: Forgot to update this when Makefile changed.
2348 :    
2349 : bates 835 2005-05-11 Douglas Bates <bates@wisc.edu>
2350 : bates 726
2351 :     * src/dgCMatrix.c (csc_transpose): Simplified function fixing a
2352 :     bug reported by Kurt Hornik and Michael Hahsler.
2353 :    
2354 : bates 835 2005-05-10 Douglas Bates <bates@wisc.edu>
2355 : bates 725
2356 :     * src/lgCMatrix.c (Matrix_lgClgCmm): Implementation of methods for
2357 :     logical sparse matrices. These will also be used in the symbolic
2358 :     analysis for lmer objects.
2359 :    
2360 :     * src/dsCMatrix.c (dsCMatrix_matrix_solve): Copied the dimensions
2361 :     of b to the result. Fixes bug reported by Jean.Coursol@math.u-psud.fr
2362 : maechler 791
2363 : bates 835 2005-05-06 Douglas Bates <bates@wisc.edu>
2364 : bates 714
2365 :     * src/dgeMatrix.c (dgeMatrix_colsums): Added an implementation of
2366 :     colMeans, colSums, rowMeans and rowSums.
2367 :    
2368 : bates 835 2005-04-18 Douglas Bates <bates@wisc.edu>
2369 : bates 692
2370 :     * src/lgCMatrix.[ch]: code for _validate method and stub for
2371 :     multiplication operation.
2372 :    
2373 :     * src/dgeMatrix.c (dgeMatrix_matrix_solve): Passing wrong argument
2374 :     to dgetrs.
2375 :    
2376 :     * src/init.c: Fix cut-and-paste error in definition of
2377 :     dgeMatrix_matrix_solve
2378 :    
2379 :     * src/{many files}: Tighten code by using ALLOC_SLOT.
2380 :    
2381 : bates 835 2005-04-15 Douglas Bates <bates@wisc.edu>
2382 : bates 692
2383 :     * R/AllClass.R: Add lgTMatrix and lgCMatrix classes
2384 :    
2385 :     * DESCRIPTION: Eliminate import of stats.
2386 :    
2387 : maechler 791
2388 : bates 835 2005-04-06 Douglas Bates <bates@wisc.edu>
2389 : bates 692
2390 :     * R/AllClass.R : add logical sparse matrix classes
2391 :    
2392 : maechler 687 2005-04-01 Martin Maechler <maechler@stat.math.ethz.ch>
2393 :    
2394 :     * R/dgTMatrix.R: add "[" method for triplet matrices
2395 :     * R/sparseMatrix.R: and other sparse ones; --> add show() for sparse
2396 :    
2397 : bates 835 2005-03-31 Douglas Bates <bates@wisc.edu>
2398 : maechler 687
2399 :     * DESCRIPTION (Version): release 0.95-5 to CRAN
2400 :    
2401 :     * R/dMatrix.R: add %*%, crossprod and solve "fallback" methods
2402 :     * R/sparseMatrix.R: %*%, crossprod()
2403 :     * R/dgeMatrix.R: more "fallback" methods for numeric/dense matrices
2404 :     * man/*.Rd: move method definitions to 'Matrix' and 'dMatrix'
2405 :     * src/lmer.c (lmer_fitted): fix thinko
2406 :    
2407 : maechler 676 2005-03-26 Martin Maechler <maechler@stat.math.ethz.ch>
2408 :    
2409 :     * R/AllClass.R: add two virtual sparse classes ``on top''
2410 :    
2411 :     2005-03-24 Martin Maechler <maechler@stat.math.ethz.ch>
2412 :    
2413 :     * R/AllClass.R (setClass): use "VIRTUAL" for the virtual classes;
2414 :     correspondingly fix examples and tests/ since new()
2415 :     doesn't work for virtual classes.
2416 :    
2417 : maechler 658 2005-03-17 Martin Maechler <maechler@stat.math.ethz.ch>
2418 :    
2419 :     * R/Matrix.R (as.matrix): method and one for unname()
2420 :     * tests/dpoMatrix.R: tests should now be less platform dependent;
2421 :     also run for R 2.1.0; using as.matrix()
2422 :    
2423 : bates 835 2005-03-15 Douglas Bates <bates@wisc.edu>
2424 : maechler 658
2425 :     * R/pMatrix.R: "pMatrix" class added
2426 :     * ....
2427 :    
2428 : bates 835 2005-03-14 Douglas Bates <bates@wisc.edu>
2429 : bates 645
2430 :     * R/dtpMatrix.R: Add unpack method and an example.
2431 :    
2432 :     * src/dsyMatrix.c (dsyMatrix_trf): Add BunchKaufman factorization
2433 :     of general symmetric matrices and associated S4 methods.
2434 :    
2435 : maechler 658 2005-03-10 Martin Maechler <maechler@stat.math.ethz.ch>
2436 :     +
2437 :     2005-03-05 Martin Maechler <maechler@stat.math.ethz.ch>
2438 :    
2439 :     * R/dgeMatrix.R (setAs): and many other files: more coercion,
2440 :     crossprod() and "%*%" methods added; tests, too.
2441 :     * tests/matprod.R: new, for testing these
2442 :    
2443 : bates 835 2005-03-03 Douglas Bates <bates@wisc.edu>
2444 : bates 599
2445 :     * src/lmer.c (lmer_fitted): Added.
2446 :    
2447 : bates 835 2005-03-02 Douglas Bates <bates@wisc.edu>
2448 : bates 596
2449 :     * R/dsTMatrix.R: Conversion from dsTMatrix to dsCMatrix
2450 :    
2451 : bates 835 2005-02-28 Douglas Bates <bates@wisc.edu>
2452 : bates 582
2453 :     * src/*.c,po/,inst/po: Internationalization and localization of
2454 :     the package.
2455 :    
2456 :     * src/ldl.[ch]: Removed these as their contents are referenced in the
2457 :     R_ldl.c file.
2458 :    
2459 :     * src/flame.[ch]: Removed these source files.
2460 : maechler 658
2461 : bates 582 * src/dtrMatrix.c (make_array_triangular): Move to Mutils
2462 :    
2463 :     * src/LU.[ch],src/init.c: absorb in factorizations
2464 :    
2465 :     * src/Mutils.h: prepare for internationalization
2466 :    
2467 :     * src/cblas.h: move the enum definitions to Mutils.h and remove
2468 :     this file
2469 :    
2470 : maechler 578 2005-02-26 Martin Maechler <maechler@stat.math.ethz.ch>
2471 :    
2472 : maechler 579 * R/dgeMatrix.R: provide "dimnames" and "dimnames<-" methods
2473 :    
2474 :     * R/dtrMatrix.R: fix t() method
2475 :    
2476 : maechler 578 * R/dgeMatrix.R: define group methods "Arith", "Math", "Math2"
2477 : maechler 658 * NAMESPACE: export them (and import generics from "methods")
2478 : maechler 578 * tests/group-methods.R : and test them.
2479 :    
2480 :     * src/dtrMatrix.c (dtrMatrix_as_dgeMatrix): prevent seg.fault in
2481 :     border case
2482 :    
2483 :     2005-02-24 Douglas Bates <bates@stat.wisc.edu>
2484 :    
2485 : maechler 658 * DESCRIPTION (Version): 0.95-2 released to CRAN
2486 : maechler 578
2487 :     * src/dgBCMatrix.c:
2488 :     * src/lmer.c: many changes
2489 :     * ...
2490 :    
2491 : maechler 512 2005-02-04 Martin Maechler <maechler@stat.math.ethz.ch>
2492 :    
2493 :     * R/Matrix.R: add more sophisticated show() method.
2494 :    
2495 : maechler 578 2005-02-02 Douglas Bates <bates@stat.wisc.edu>
2496 :    
2497 :     * */* : almost complete reorganization of classes.
2498 :    
2499 : bates 835 2005-01-26 Douglas Bates <bates@wisc.edu>
2500 : bates 460
2501 :     * R/AllGeneric.R: Added matrix exponential generic expm and a method
2502 :     for the geMatrix class.
2503 :    
2504 : bates 835 2005-01-24 Douglas Bates <bates@wisc.edu>
2505 : bates 460
2506 :     * src/Makefile (clean): Remove *.a and *.so
2507 :    
2508 :     * man/cscBlocked-class.Rd: Remove reference to the lmer-class.
2509 :    
2510 : bates 835 2005-01-23 Douglas Bates <bates@wisc.edu>
2511 : bates 460
2512 : maechler 658 * src/lmer.c (Lind): Definition of Lind was backwards. This only
2513 : bates 460 had an effect in cases with more than 2 grouping factors.
2514 :    
2515 : bates 835 2005-01-03 Douglas Bates <bates@wisc.edu>
2516 : bates 415
2517 :     * src/lmeRep.c (lmer_variances): change from lmeRep to lmer
2518 :    
2519 : bates 835 2004-12-23 Douglas Bates <bates@wisc.edu>
2520 : bates 410
2521 :     * src/init.c (R_init_Matrix): Reorder calls to R_registerRoutines
2522 :     and R_useDynamicSymbols (suggested by B.D.Ripley).
2523 :    
2524 : bates 835 2004-12-14 Douglas Bates <bates@wisc.edu>
2525 : bates 392
2526 :     * R/sscMatrix.R: Add determinant methods
2527 :    
2528 :     * src/triplet.[ch],src/init.c (triplet_to_matrix): Add a coercion
2529 :     for tripletMatrix to matrix.
2530 :    
2531 : bates 835 2004-12-13 Douglas Bates <bates@wisc.edu>
2532 : bates 388
2533 : bates 392 * R/AllClass.R (.onLoad): Eliminate the bbCrosstab class, which is
2534 :     no longer used.
2535 :    
2536 : bates 388 * src/R_ldl.c: Created an R-specific version of the ldl.[ch] files
2537 :     with dynamic allocation of scratch arrays.
2538 :    
2539 :     * src/ssclme.c (ssclme_copy_ctab): Fixed bug in creation of ZtZ
2540 :     for multivariate random effects with multiple grouping factors.
2541 :     Fixes part but not all of #15.
2542 :    
2543 : bates 835 2004-12-03 Douglas Bates <bates@wisc.edu>
2544 : bates 375
2545 :     * src/lmeRep.c (lmeRep_factor): order of operations for multiple
2546 :     scalar grouping factors corrected.
2547 :    
2548 : bates 835 2004-11-29 Douglas Bates <bates@wisc.edu>
2549 : bates 375
2550 :     * src/bCrosstab.c: remove diag_update which is no longer used
2551 :    
2552 : bates 835 2004-11-16 Douglas Bates <bates@wisc.edu>
2553 : bates 350
2554 :     * src/Metis_utils.c: Move metis.h include to C sources so that the
2555 :     .h file can be included.
2556 :    
2557 : bates 835 2004-11-12 Douglas Bates <bates@wisc.edu>
2558 : bates 342
2559 : bates 350 * src/LU.c,geMatrix.c,trMatrix.c, etc.:
2560 : bates 342 Complete allocation of slots in NEW_OBJECT.
2561 :    
2562 :     * src/Mutils.h: Moved list of symbols to an include file
2563 :    
2564 : bates 835 2004-11-11 Douglas Bates <bates@wisc.edu>
2565 : bates 342
2566 :     * src/geMutils.c (Matrix_init): remove unused function
2567 :    
2568 : bates 835 2004-11-10 Douglas Bates <bates@wisc.edu>
2569 : bates 342
2570 :     * src/cscMatrix.c (csc_to_imagemat): removed unused function
2571 :    
2572 : bates 835 2004-11-05 Douglas Bates <bates@wisc.edu>
2573 : bates 327
2574 :     * src/Makefile.win (SOURCES_C): Keep consistent with Makefile
2575 :    
2576 : bates 835 2004-10-27 Douglas Bates <bates@wisc.edu>
2577 : bates 303
2578 :     * R/pdmatrix.R: remove PACKAGE="Matrix" in .Call calls
2579 :    
2580 : bates 835 2004-10-04 Douglas Bates <bates@wisc.edu>
2581 : bates 296
2582 :     * src/init.c: Created R_init_Matrix and added registration of C
2583 :     routines.
2584 :    
2585 : bates 835 2004-10-02 Douglas Bates <bates@wisc.edu>
2586 : bates 283
2587 :     * R/tripletMatrix.R: Force a require(lattice) for the image methods.
2588 :    
2589 : bates 835 2004-06-15 Douglas Bates <bates@wisc.edu>
2590 : bates 229
2591 :     * man/trMatrix-class.Rd: Escape the % chars in .Rd files.
2592 :    
2593 : bates 111 2004-04-20 Douglas Bates <bates@stat.wisc.edu>
2594 :    
2595 :     * src/Makefile.win ($(SHLIB)): Modifications per Uwe Ligges.
2596 :    
2597 : bates 109 2004-04-19 Douglas Bates <bates@stat.wisc.edu>
2598 :    
2599 :     * src/ssclme.c (ssclme_update_mm): fix logic error in
2600 :     ssclme_update_mm
2601 :    
2602 : bates 105 2004-04-18 Douglas Bates <bates@stat.wisc.edu>
2603 :    
2604 :     * src/ssclme.c (ssclme_coef, ssclme_coefGets): Create consistency
2605 :     in the order of unconstrained and constrained parameters.
2606 :     (ssclme_gradient): Added the gradients (not yet correct for
2607 :     multidimensional, unconstrained case).
2608 :    
2609 : bates 78 2004-04-14 Douglas Bates <bates@stat.wisc.edu>
2610 :    
2611 :     * src/ssclme.c (ssclme_EMsteps): Fix logic in REML update
2612 :    
2613 :     * src/Makefile.win: Remove unneeded ranlib call
2614 :    
2615 : bates 71 2004-04-12 Douglas Bates <bates@stat.wisc.edu>
2616 :    
2617 :     * DESCRIPTION (Version): New release
2618 :    
2619 :     * src/Makefile.win: Update Makefile.win to umfpack removal.
2620 :    
2621 : bates 49 2004-04-05 Douglas Bates <bates@bates2_home>
2622 :    
2623 :     * src/triplet_to_col.c: Create triplet_to_col as a native
2624 : maechler 658 function, not the version from umfpack. There were problems with
2625 : bates 49 the configuration of UMFPACK for 64-bit processors and there was
2626 :     only one umfpack routine being used so I moved it here.
2627 :    
2628 : bates 45 2004-04-04 Douglas Bates <bates@bates2_home>
2629 :    
2630 :     * src/ssclme.c (ssclme_variances): New function.
2631 :    
2632 : bates 28 2004-03-28 Douglas Bates <bates@bates2_home>
2633 :    
2634 :     * src/ssclme.c (ssclme_fitted): Added function.
2635 :    
2636 : bates 22 2004-03-27 Douglas Bates <bates@bates2_home>
2637 :    
2638 :     * src/ssclme.c (ssclme_transfer_dimnames): Add new function to
2639 :     store the dimnames in the XtX and bVar slots
2640 :     (ssclme_update_mm): Change the dimensions of the bVar slot
2641 :     components and the returned value from ssclme_ranef.
2642 :    
2643 : bates 10 2004-03-18 Douglas Bates <bates@stat.wisc.edu>
2644 :    
2645 :     * R/{pdMat.R,pdIdent.R,pdLogChol.R,pdMatrixLog.R,pdNatural.R},
2646 :     src/{pdMat.c,pdIdent.c,pdLogChol.c,pdNatural.c},
2647 :     tests/{pdCompSymm.R,pdDiag.R,pdIdent.R,pdLogChol.R,pdNatural.R},
2648 :     man/{pdMat-class.Rd,pdmatrix-class.Rd,corrmatrix-class.Rd,
2649 :     pdDiag-class.Rd,pdIdent-class.Rd,pdNatural-class.Rd,
2650 :     pdLogChol-class.Rd,coefGets.Rd,pdCompSymm-class.Rd,
2651 :     pdfactor-class.Rd,pdFactor.Rd,pdMatrix.Rd,
2652 :     pdBlocked-class.Rd},AllClass.R,AllGeneric.R:
2653 :     Moved the pdMat classes from the lme4 package.
2654 :    
2655 :     2004-03-02 Douglas Bates <bates@stat.wisc.edu>
2656 :    
2657 :     * man/ssclme-class.Rd: Update definition and documentation of the
2658 :     ssclme class to include the DIsqrt slot.
2659 :    
2660 :     * src/ssclme.c (ssclme_deviance): Modify order of computation
2661 :     (much faster using dsyrk, a level 3 BLAS routine).
2662 :    
2663 :     * src/Makefile (SUBLIBS): Change definition (K. Hornik)
2664 :    
2665 :     2004-02-28 Douglas Bates <bates@stat.wisc.edu>
2666 :    
2667 :     * tests/ssclme.R: Modify the test to account for the permutation
2668 :     of the levels of the grouping factors.
2669 :    
2670 :     2004-02-23 Douglas Bates <bates@stat.wisc.edu>
2671 :    
2672 :     * R/ssclme.R,src/ssclme.c (ssclme): Move slots of sscCrosstab slot
2673 :     directly into the ssclme class definition.
2674 :    
2675 :     2004-02-22 Douglas Bates <bates@stat.wisc.edu>
2676 :    
2677 :     * DESCRIPTION (Date): New release
2678 :    
2679 :     * man/ssclme-class.Rd: new file.
2680 :    
2681 :     * src/ssclme.c (ssclme_loglik): major revisions in design. It
2682 :     works and it's fast!
2683 :    
2684 :     2004-02-17 Douglas Bates <bates@stat.wisc.edu>
2685 :    
2686 :     * src/taucs/Makefile.win (lib): Change "ar" to "$(AR)" (B.Ripley)
2687 :    
2688 :     2004-02-16 Douglas Bates <bates@stat.wisc.edu>
2689 :    
2690 :     * DESCRIPTION (Date): New release
2691 :    
2692 :     * NAMESPACE: Don't export ssclme.
2693 :    
2694 :     * data/ScotsSec.rda, man/ScotsSec.Rd: Add Scottish secondary
2695 :     school data.
2696 :    
2697 :     2004-02-11 Douglas Bates <bates@stat.wisc.edu>
2698 :    
2699 :     * src/sscCrosstab.c (sscCrosstab): Added a row to the incidence to
2700 :     keep track of the fixed-effects and the response. Counts also
2701 :     gets an extra element, which is always one.
2702 :    
2703 :     * src/ldl.c: Include these routines from Tim Davis' LDL package.
2704 :    
2705 :     2004-02-10 Douglas Bates <bates@stat.wisc.edu>
2706 :    
2707 :     * src/cscMatrix.c (csc_transpose): new function
2708 :    
2709 :     * src/Mutils.c (csc_sort_columns): perm/iperm confusion corrected
2710 :     (csc_components_transpose): new function
2711 :    
2712 :     2004-02-06 Douglas Bates <bates@stat.wisc.edu>
2713 :    
2714 :     * src/triplet.c (triplet_validate): Fix Dim slot on generated
2715 :     triplets
2716 :    
2717 :     2004-01-30 Douglas Bates <bates@stat.wisc.edu>
2718 :    
2719 :     * R/sscCrosstab.R (sscCrosstab): Added sscCrosstab generator function.
2720 :    
2721 :     * src/LU.h (MATRIX_LU_H): Add #ifndef #define ... #endif to this
2722 :     and all other .h files in src.
2723 :    
2724 :     * src/Makefile.win: This and other Makefile.win files contributed
2725 :     by Brian Ripley.
2726 :    
2727 :     2004-01-27 Douglas Bates <bates@stat.wisc.edu>
2728 :    
2729 :     * R/syMatrix.R: Added methods for "%*%".
2730 :    
2731 :     * R/Hilbert.R (Hilbert): Changed Hilbert function to return a
2732 :     poMatrix object.
2733 :    
2734 :     2004-01-26 Douglas Bates <bates@stat.wisc.edu>
2735 :    
2736 :     * man/sscChol-class.Rd,man/mm.Rd,man/y.Rd: Added man pages.
2737 :    
2738 :     2004-01-25 Douglas Bates <bates@bates2_home>
2739 :    
2740 :     * inst/doc/Introduction.Rnw,Comparisons.Rnw: Added vignettes.
2741 :    
2742 :     * R/csc.R: Convert all cscMatrix classes to use Dim slot instead
2743 :     of nrow.
2744 :    
2745 :     2003-12-31 Douglas Bates <bates@stat.wisc.edu>
2746 :    
2747 :     * src/taucs/taucs.h: Moved taucs.h, amd.h, and umfpack.h into
2748 :     subdirectories.
2749 :    
2750 :     2003-12-08 Douglas Bates <bates@stat.wisc.edu>
2751 :    
2752 :     * src/taucs.h: Accidently referred to global header files
2753 :     instead of local files.
2754 :    
2755 :     2003-12-04 Douglas Bates <bates@stat.wisc.edu>
2756 :    
2757 :     * R/AllClass.R: Lots of changes. Removed all the lapack++ code
2758 :     and methods and replaced all classes with S4 classes.
2759 :    
2760 :     2003-04-19 Douglas Bates <bates@stat.wisc.edu>
2761 :    
2762 :     * R/det.R,man/det.Rd: Change name of det generic to determinant
2763 :    
2764 :     * src/R_LapackPP.cc: Change method of calculating determinants
2765 :    
2766 :     2003-02-03 Douglas Bates <bates@stat.wisc.edu>
2767 :    
2768 :     * DESCRIPTION (Version): removed empty data directory as requested
2769 :     by CRAN maintainers. Changed version number and date.
2770 :    
2771 :     2002-10-23 Douglas Bates <bates@stat.wisc.edu>
2772 :    
2773 :     * src/laindex.h: Applied patches from Brian Ripley for compilation
2774 :     under Windows.
2775 :    
2776 :     * Added configure.win and src/Makevars.win as requested by Brian
2777 :     Ripley.
2778 :    
2779 :     2002-05-03 Douglas Bates <bates@stat.wisc.edu>
2780 :    
2781 :     * src/lamatrix.h: Removing pre-1.2.0 compatibility code per Kurt
2782 :     Hornik.
2783 :    
2784 :     2002-04-24 Douglas Bates <bates@stat.wisc.edu>
2785 :    
2786 :     * configure.ac: Replaced configure.in with configure.ac
2787 :     contributed by Kurt Hornik.
2788 :    
2789 :     * aclocal.m4 (ac_clean_files): Replaced this with Kurt Hornik's
2790 :     version for R-1.5.0
2791 :    
2792 : maechler 512
2793 : bates 10 2001-12-10 Douglas Bates <bates@stat.wisc.edu>
2794 :    
2795 :     * man/eigen.Rd: Removed the .Alias in the example

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