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Annotation of /pkg/ChangeLog

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Revision 2154 - (view) (download)

1 : maechler 2154 2008-03-22 Martin Maechler <maechler@stat.math.ethz.ch>
2 :    
3 :     * src/dsCMatrix.c (dsCMatrix_LDL_D): cleanup, also using
4 :     internal_chm_factor().
5 :    
6 :     * R/AllGeneric.R: do *not* define a "chol" generic
7 :     (but rather use the implicit one *without* making pivot
8 :     part of the signature)
9 :     * R/*.R: drop the 'pivot' from chol's signature and make
10 :     'pivot=FALSE' a default argument of method definitions.
11 :    
12 :     * .Rbuildignore: add 'wrld_1deg': I.e. do not put it into released
13 :     version of Matrix
14 :    
15 : maechler 2139 2008-03-18 Martin Maechler <maechler@stat.math.ethz.ch>
16 :    
17 : maechler 2144 * R/Tsparse.R (.T.2.n): drop 0's before coercion to "nMatrix"
18 :    
19 :     * R/sparseMatrix.R (is.na): new simple method
20 :     * R/denseMatrix.R (is.na): ditto.
21 :    
22 :     * R/diagMatrix.R (.symDiagonal): newly exported utility.
23 :    
24 :     * R/diagMatrix.R (Ops): <diag> * <numeric> should not become dgeMatrix!
25 :    
26 : maechler 2139 * src/UFsparse_download.sh: -->
27 :     * src/CHOLMOD/: update to CHOLMOD version 1.6 (Nov.2007)
28 :    
29 : maechler 2137 2008-03-17 Martin Maechler <maechler@stat.math.ethz.ch>
30 :    
31 :     * src/dsCMatrix.c (dsCMatrix_LDL_D): even faster utility with same
32 :     functionality; barely tested in
33 :     * tests/factorizing.R
34 :    
35 :     * src/Csparse.c (diag_tC): new functionality to enable faster
36 :     determinant(<dsCMatrix>, .) in
37 :     * R/dsCMatrix.R
38 :    
39 :     2008-03-17 18:53 Douglas Bates <bates@stat.wisc.edu>
40 :    
41 :     * R/CHMfactor.R, inst/include/Matrix.h, inst/include/Matrix_stubs.c,
42 :     src/CHMfactor.c, src/CHMfactor.h,
43 :     man/CHMfactor-class.Rd, src/init.c, tests/factorizing.R:
44 :     Log-determinant of the parent matrix from a CHMfactor object as
45 :     chm_factor_ldetL2; documentation and support
46 :    
47 :     2008-03-15 Martin Maechler <maechler@stat.math.ethz.ch>
48 :    
49 :     * R/dsCMatrix.R: enable determinant(<dsCMatrix>, .) via chol(.)
50 :    
51 : maechler 2130 2008-03-14 Martin Maechler <maechler@stat.math.ethz.ch>
52 :    
53 :     * R/dsCMatrix.R: setAs(., "dsCMatrix") but with a deprecation
54 :     warning.
55 :    
56 : maechler 2128 2008-03-13 Martin Maechler <maechler@stat.math.ethz.ch>
57 :    
58 :     * DESCRIPTION (Version, Date): bug-fix release 0.999375-6
59 :    
60 :     * R/diagMatrix.R (diag2tT.u): utility to be smarter in
61 :     <diagonal> o <sparse_triangular>
62 :     setAs(., "nMatrix") added.
63 :    
64 :     * R/diagMatrix.R (Diagonal): Diagonal(4, x=3) now works too
65 :    
66 :     * R/Auxiliaries.R (.diagU2N): more careful coercion in 2 steps
67 :     new argument 'checkDense = FALSE'.
68 :    
69 :    
70 : maechler 2125 2008-03-07 Martin Maechler <maechler@stat.math.ethz.ch>
71 :    
72 : maechler 2127 * src/dgeMatrix.c (dgeMatrix_exp): fix the octave-origin bug in the
73 :     back-permutation of the matrix exponential.
74 :    
75 :     * tests/matr-exp.R: test the fix (for an example where expm() was wrong).
76 :    
77 : maechler 2126 * DESCRIPTION (Date,Version): ready to release 0.999375-5
78 :    
79 : maechler 2125 * tests/simple.R: testing diagN2U
80 :    
81 :     2008-03-06 Martin Maechler <maechler@stat.math.ethz.ch>
82 :    
83 :     * R/Auxiliaries.R (diagN2U): interface to
84 :    
85 :     * src/Csparse.c (Csparse_diagN2U): .Call()able SEXP version of chm_diagN2U()
86 :    
87 :     * tests/matprod.R: test for triangularity preserving <dtC> %*% <dtC>
88 :    
89 : maechler 2123 2008-03-05 Martin Maechler <maechler@stat.math.ethz.ch>
90 :    
91 : maechler 2125 * src/chm_common.c (chm_diagN2U): new utility.
92 :    
93 :     * src/Csparse.c (Csparse_Csparse_crossprod, Csparse_Csparse_prod):
94 :     make use of chm_diagN2U() and hence now preserve triangularity and
95 :     unit-triangularity.
96 :    
97 : maechler 2123 * DESCRIPTION (LicenseDetails): new; such that 'License:' becomes "canonical"
98 :    
99 : maechler 2120 2008-03-04 Martin Maechler <maechler@stat.math.ethz.ch>
100 :    
101 :     * R/diagMatrix.R (subDiag): fix when x[..] became a vector
102 :    
103 :     * src/Tsparse.c (Tsparse_diagU2N): new utility, necessary for e.g.
104 :     * src/Csparse.c (Csparse_crossprod): use [CT]sparse_diagU2N() !!
105 :    
106 :     * R/Auxiliaries.R (.diagU2N): make use of new Tsparse_diagU2N
107 :    
108 :     * R/Ops.R ("-" (<sparseMatrix>)): use diagU2N()
109 :    
110 :     * src/chm_common.c (AS_CHM_FINISH): add note about problem
111 :     for triangular (diag = "U").
112 :    
113 : maechler 2115 2008-02-21 Martin Maechler <maechler@stat.math.ethz.ch>
114 :    
115 :     * R/Auxiliaries.R (as_Csparse2): drop this, replacing by
116 :     * R/bind.R: .Call(dense_to_Csparse, *)
117 :    
118 :     2008-02-20 Martin Maechler <maechler@stat.math.ethz.ch>
119 :    
120 :     * R/Matrix.R (Matrix): no longer use coercions to specific classes
121 :     (since we are discouraging them in user code).
122 :    
123 :     * tests/*.R: also replaces coercions to specific classes by
124 :     coercions to super classes.
125 :    
126 :     * R/denseMatrix.R (.dense2C): simplified by using forceSymmetric()
127 :    
128 :    
129 :     2008-02-19 Martin Maechler <maechler@stat.math.ethz.ch>
130 :    
131 :     * man/CAex.Rd: example: coerce to symmetric*, not dsC*
132 :    
133 :     * src/dense.c (dense_band): generalized from ddense_band
134 :    
135 :     * R/ddenseMatrix.R (.trilDense,.triuDense, .bandDense):
136 :     now for "denseMatrix" (instead of just "ddense*"); much
137 :     simplified setMethod()s for these.
138 :    
139 :     * src/dense.c (dense_to_symmetric): generalized from ddense_*
140 :    
141 :     2008-02-18 Martin Maechler <maechler@stat.math.ethz.ch>
142 :    
143 :     * R/AllGeneric.R: forceSymmetric() generic: fast no-checking
144 :     version of as(*, "symmetricMatric").
145 :    
146 :     * src/dense.c (ddense_to_symmetric): add 'symm_test' argument, and
147 :     * R/symmetricMatrix.R: set it TRUE in coercion to "symmetricMatrix"
148 :    
149 : maechler 2113 2008-02-16 Martin Maechler <maechler@stat.math.ethz.ch>
150 :    
151 :     * R/Matrix.R (subset.ij): utility, as first step to faster
152 :     M [ <ij-matrix> ] indexing.
153 :    
154 :     * R/Matrix.R (.M.sub.i.logical): M[ <logical> ] : try better.
155 :    
156 :     * src/dense.c (ddense_symmpart, ddense_skewpart): new functions
157 :     for more efficient symmpart() and skewpart() methods.
158 :    
159 :     * src/Mutils.c (equal_string_vectors): utility
160 :    
161 :     * src/dense.c (ddense_to_symmetric): new function used in
162 :    
163 :     * R/symmetricMatrix.R: setAs(., "symmetricMatrix")
164 :    
165 :     * R/sparseMatrix.R, et_al (isSymmetric): add '...' to formals, in
166 :     order to match the generic (and evade .local(..)).
167 :    
168 :     * R/dsCMatrix.R: dgC -> dsC: use C code!
169 :    
170 :     * NAMESPACE, R/AllGeneric.R (symmpart, skewpart): new functions
171 :     as per TODO
172 :    
173 :     * R/Auxiliaries.R (setZero, all0Matrix): new utilities
174 :    
175 :     * R/symmetricMatrix.R: obvious symmpart(), skewpart() methods
176 :    
177 :    
178 :     2008-02-15 Martin Maechler <maechler@stat.math.ethz.ch>
179 :    
180 :     * R/Ops.R (.Arith.Csparse): use diagU2N when needed in triangular
181 :    
182 :     * R/Auxiliaries.R (non0.i): take out of non0ind
183 :    
184 :     * R/ddenseMatrix.R (.trilDense, .triuDense, .bandDense):
185 :     make tril(), triu(), band() work for "matrix" and all "dense*"
186 :    
187 :     * R/triangularMatrix.R (.tri[lu].tr): need .diagU2N(*)
188 :     * tests/simple.R: test the fix above
189 :    
190 :     * R/sparseMatrix.R ([): simplification: no coerce to <general>
191 :     before we use as(., <Tsparse>)[...] anyway
192 :    
193 :     * R/Rsparse.R (.viaC.to.R): mostly instead of .viaC.to.dgR()
194 :    
195 :     * R/triangularMatrix.R (isTriangular): methods for all subclasses
196 :     instead of "triangularMatrix" -- just to disambiguate
197 :    
198 :     2008-02-14 Martin Maechler <maechler@stat.math.ethz.ch>
199 :    
200 :     * tests/Class+Meth.R (dotestMat): add m[FALSE, FALSE] { <-> TODO}
201 :     * tests/indexing.R: example that fails above
202 :    
203 : maechler 2110 2008-01-26 Martin Maechler <maechler@stat.math.ethz.ch>
204 :    
205 :     * R/Matrix.R (.M.sub.i.2col): fix for logical matrix indexing
206 :     * R/Tsparse.R (.TM.sub.i.2col, .TM.repl.i.2col): ditto;
207 :     now, M[lower.tri(M)] and M[lower.tri(M)] <- v work better
208 :    
209 :     * src/Tsparse.c (Tsparse_to_tCsparse): new fast utility.
210 :     * src/Tsparse.h, init.c: ditto
211 :     * R/Auxiliaries.R (isTriT): new; faster than going via Csparse
212 :     both isTriC() and isTriT() now return TRUE with "kind" or FALSE.
213 :     * R/sparseMatrix.R (isTriangular): hence simplified
214 :    
215 : maechler 2108 2008-01-24 Martin Maechler <maechler@stat.math.ethz.ch>
216 :    
217 :     * R/Ops.R (.Arith.Csparse): new utility factored out of former
218 :     <dgC> o <dgC>, extended for triangular and also used in <dtC> o <dtC>.
219 :    
220 : maechler 2106 2008-01-23 Martin Maechler <maechler@stat.math.ethz.ch>
221 :    
222 :     * tests/factorizing.R (checkSchur): and more tests for checking Schur()
223 :    
224 : maechler 2108 * inst/test-tools.R (isOrthogonal): new function; also file restructured
225 : maechler 2106
226 :     2008-01-22 Martin Maechler <maechler@stat.math.ethz.ch>
227 :    
228 :     * R/ngTMatrix.R: allow as(<numeric matrix>, "ngTMatrix") and hence
229 :     coercion to "nMatrix" and "pMatrix"
230 :    
231 :     * R/AllClass.R: "Schur" class; "number" class union
232 :     * man/number-class.Rd:
233 :     * man/Schur-class.Rd:
234 :    
235 :     * R/eigen.R (.dgeSchur): utility, and return "Schur" class
236 :     (.simpleSchur): Schur() method for diagonal matrices
237 :     (.triSchur): Schur() method for triangular matrices
238 :     (Schur.sym): Schur() for symmetric matrices {building on eigen()}.
239 :    
240 :    
241 :     2008-01-21 Martin Maechler <maechler@stat.math.ethz.ch>
242 :    
243 :     * src/dgCMatrix.c (dgCMatrix_QR): set @Dim slot (as per doc)
244 :    
245 : maechler 2105 2008-01-15 Martin Maechler <maechler@stat.math.ethz.ch>
246 :    
247 :     * R/CHMfactor.R (solve): method for b="numeric", but also b="ANY"
248 :     in order to ensure 'system = *' is not lost;
249 :     formals()$system instead of cut&paste.
250 :     * tests/factorizing.R: test solve(<CHM..>, <numeric>)
251 :    
252 : maechler 2102 2008-01-11 Martin Maechler <maechler@stat.math.ethz.ch>
253 : maechler 2096
254 : maechler 2105 * DESCRIPTION (Date): make ready for release --> 0.999375-4
255 : maechler 2096
256 : maechler 2102 * R/dgeMatrix.R: fix rcond() method for "dgeMatrix".
257 : maechler 2096
258 : maechler 2098 2007-12-08 Martin Maechler <maechler@stat.math.ethz.ch>
259 : maechler 2096
260 : maechler 2098 * R/pMatrix.R: as(*, "matrix") now returns 0/1 *integer* matrix,
261 :     and hence does as.vector(.).
262 :     * man/pMatrix-class.Rd: docs
263 :     * R/sparseMatrix.R: fix for printing "integer sparse"
264 :    
265 :     * tests/Class+Meth.R (tstMatrixClass): test M[FALSE], M[2] etc
266 :    
267 :     * R/Matrix.R and others: use "exact" function argument list for
268 :     both "[" : (x, i,j, ..., drop)
269 :     and "[<-" : (x, i,j, ..., value)
270 :    
271 :     * R/denseMatrix.R: M[i] and M[i] <- v (i vector) now work
272 :     * R/Tsparse.R (replTmat): ditto
273 :     * R/diagMatrix.R (replDiag): ditto
274 :     * R/Csparse.R (replCmat): ditto {was it worth the pain?}
275 :     * tests/indexing.R: testing the above
276 :    
277 : maechler 2096 2007-12-07 Martin Maechler <maechler@stat.math.ethz.ch>
278 :    
279 :     * R/sparseMatrix.R (cov2cor): method for sparse matrices
280 :    
281 :     * R/diagMatrix.R ([<-): fix D[ cbind(i,j) ] <- v
282 :    
283 :     * R/bind2.R: fix for Rsparse* and rbind2(dense,dense)
284 :    
285 :     * tests/Class+Meth.R: test cbind2, rbind2 and diag<-
286 :    
287 :     2007-12-06 Martin Maechler <maechler@stat.math.ethz.ch>
288 :    
289 :     * R/Matrix.R: "generic" cov2cor() method
290 :    
291 :     * R/nearPD.R: new 'only.values', 'keepDiag' arguments;
292 :     speed up Q %*% D %*% t(Q)
293 :     * tests/dpoMatrix.R: test nearPD()
294 :    
295 :     2007-12-05 Doug Bates and Martin Maechler
296 :    
297 :     * R/sparseMatrix.R: xtabs(*, sparse=.) function; an extention of
298 :     stats::xtabs() allowing to create sparse matrices.
299 :    
300 :     2007-10-08 Martin Maechler <maechler@stat.math.ethz.ch>
301 :    
302 :     * DESCRIPTION (Version): *-4 (released *-3 two days ago)
303 :    
304 : maechler 2081 2007-10-06 Martin Maechler <maechler@stat.math.ethz.ch>
305 :    
306 :     * R/pMatrix.R: solve(<Matrix>, <pMatrix>)
307 :    
308 :     2007-10-05 Martin Maechler <maechler@stat.math.ethz.ch>
309 :    
310 :     * R/LU.R: solve() method for "denseLU"
311 :    
312 :     2007-10-01 Martin Maechler <maechler@stat.math.ethz.ch>
313 :    
314 :     * DESCRIPTION (Version): 0.999375-3 preparing for release
315 :    
316 :     * R/AllGeneric.R: simplify if(.) .. else .. for R <= 2.5.1
317 :    
318 :     * R/Matrix.R (Matrix): .Internal(matrix(..)) different for R >= 2.7.0
319 :    
320 : maechler 2073 2007-09-26 Martin Maechler <maechler@stat.math.ethz.ch>
321 :    
322 :     * R/pMatrix.R (.m.mult.pMat): fix <matrix> %*% <pMatrix>,
323 :     thanks to Kasper Kristensen.
324 :     * tests/matprod.R: regression test for that.
325 :    
326 : bates 2069 2007-09-23 17:32 Douglas Bates <bates@stat.wisc.edu>
327 :    
328 :     * [r4778] R/AllGeneric.R: Check R version before defining generics for
329 :     primitives
330 :    
331 : maechler 2073 2007-09-13 Martin Maechler <maechler@stat.math.ethz.ch>
332 :    
333 :     * R/denseMatrix.R (rcond): method
334 :     * R/sparseQR.R (rcond): method, use x or t(x)
335 :    
336 :     2007-09-12 Martin Maechler <maechler@stat.math.ethz.ch>
337 :    
338 :     * R/dgeMatrix.R (rcond): method: work via qr.R() for non-square
339 :     matrices.
340 :     * R/sparseMatrix.R: Ditto for all other rcond() method definitions.
341 :    
342 :     * man/rcond.Rd: mention the more general definition, and add
343 :     example for non-square matrices.
344 :    
345 :     * man/chol.Rd: new file, for the S4 chol() generic and all methods.
346 :    
347 :     2007-09-11 Martin Maechler <maechler@stat.math.ethz.ch>
348 :    
349 :     * R/sparseQR.R: add qr.R() method [to be used for rcond()]
350 :    
351 : maechler 2062 2007-09-01 Martin Maechler <maechler@stat.math.ethz.ch>
352 :    
353 :     * R/Matrix.R ([<-): add (Matrix,missing,ANY,Matrix) etc
354 :     * tests/indexing.R: add new regression for the above cases.
355 :    
356 : maechler 2061 2007-08-30 Martin Maechler <maechler@stat.math.ethz.ch>
357 :    
358 :     * src/Mutils.h (__sun): clause for alloca.h on Solaris
359 :    
360 : maechler 2056 2007-08-16 Martin Maechler <maechler@stat.math.ethz.ch>
361 :    
362 :     * DESCRIPTION (Date, Version): 0.999375-2
363 :    
364 :     2007-08-15 Martin Maechler <maechler@stat.math.ethz.ch>
365 :    
366 :     * R/HBMM.R (readMM): make work for pattern matrices as well
367 :    
368 : bates 2050 2007-08-14 13:07 Douglas Bates <bates@stat.wisc.edu>
369 :    
370 :     * [r4730] src/Mutils.h: declare alloca
371 :     * [r4734] NAMESPACE, R/AllGeneric.R, R/Csparse.R, R/HBMM.R, R/Tsparse.R,
372 :     R/dgCMatrix.R, R/dgTMatrix.R, R/dsCMatrix.R, R/dsTMatrix.R,
373 :     man/externalFormats.Rd, src/Csparse.c, src/Csparse.h, src/DEPS.mkf,
374 :     src/HBMM.c, src/HBMM.h, src/Mutils.h, src/SOURCES_C.mkf, src/init.c,
375 :     src/mmio.c, src/mmio.h: Remove deprecated function writeHB and its
376 :     methods; switch writeMM to use CHOLMOD code; repair readMM
377 :    
378 : maechler 2048 2007-08-14 Martin Maechler <maechler@stat.math.ethz.ch>
379 :    
380 :     * R/nearPD.R, man/nearPD.Rd (nearPD): new function built on Jens
381 :     Oehlschlaegel's ... result type still to be discussed!
382 :    
383 : maechler 2043 2007-08-10 Martin Maechler <maechler@stat.math.ethz.ch>
384 :    
385 :     * man/image-methods.Rd: new, combining all image() methods
386 :    
387 :     2007-08-09 Martin Maechler <maechler@stat.math.ethz.ch>
388 :    
389 :     * R/dgCMatrix.R: define qr() and lu() methods for "sparseMatrix"
390 :     to work via dgC...
391 :    
392 :     * R/Matrix.R (Matrix): special treatment for "table" (S3)
393 :    
394 :     2007-08-07 Martin Maechler <maechler@stat.math.ethz.ch>
395 :    
396 :     * R/dgTMatrix.R (image): change defaults to
397 :     aspect = "iso", colorkey = FALSE
398 :    
399 : maechler 2039 2007-08-06 Martin Maechler <maechler@stat.math.ethz.ch>
400 :    
401 :     * src/dsyMatrix.c (dsyMatrix_matrix_mm): 'b' might be matrix;
402 :     must copy its *expanded* x slot before LAPACK call.
403 :    
404 :     * tests/matprod.R: test the last days' changes.
405 :    
406 : bates 2041 2007-08-06 16:43 Douglas Bates <bates@stat.wisc.edu>
407 :    
408 :     * [r4712] inst/include/Matrix_stubs.c: Change R_cholmod_printf in stubs
409 :     as well as in sources
410 : bates 2050 * [r4713] src/dsyMatrix.c: Duplicate the contents of the RHS before
411 :     Lapack call
412 : maechler 2043
413 : maechler 2036 2007-08-03 Martin Maechler <maechler@stat.math.ethz.ch>
414 :    
415 :     * R/Matrix.R (%*%, crossprod, tcrossprod): add method for
416 : maechler 2039 ("Matrix", "matrix") which is needed in some cases.
417 :     Ditto for solve().
418 : maechler 2036
419 :     * R/colSums.R (.as.dge.Fun): need ddenseMatrix methods to avoid
420 :     infinite recursion in dispatch for some cases.
421 :    
422 : bates 2041 2007-08-02 08:48 Martin Maechler <maechler@stat.math.ethz.ch>
423 : maechler 2036
424 : bates 2041 * [r4693] src/chm_common.c: R_cholmod_printf() instead of Rprintf() just
425 :     so pointers match
426 :    
427 : maechler 2024 2007-08-02 Martin Maechler <maechler@stat.math.ethz.ch>
428 :    
429 : maechler 2036 * DESCRIPTION (Date): set ready for release -- 0.999375-1
430 : maechler 2024
431 : bates 2020 2007-08-01 15:44 Douglas Bates <bates@stat.wisc.edu>
432 :    
433 :     * [r4686] inst/include/Matrix.h, inst/include/Matrix_stubs.c,
434 :     src/chm_common.c, src/chm_common.h: Change API for
435 :     numeric_as_chm_dense and N_AS_CHM_DN
436 : maechler 2024
437 : maechler 2018 2007-08-01 Martin Maechler <maechler@stat.math.ethz.ch>
438 :    
439 :     * src/dtrMatrix.c (dtrMatrix_matrix_mm): fix dimensionality check (!)
440 :     * tests/matprod.R: regr.test for it
441 :    
442 : maechler 2011 2007-07-20 Martin Maechler <maechler@stat.math.ethz.ch>
443 :    
444 :     * R/dMatrix.R: fix from Brian for Math2(., digits = "missing")
445 :     * tests/group-methods.R: and regression-test it
446 :    
447 : bates 2008 2007-07-19 19:45 Douglas Bates <bates@stat.wisc.edu>
448 :    
449 :     * [r4642] inst/include/Matrix.h, inst/include/Matrix_stubs.c,
450 :     inst/include/cholmod.h, src/chm_common.c, src/init.c: Export
451 :     triplet_to_sparse, documentation, use typedefs
452 : maechler 2011
453 : maechler 2005 2007-07-18 Martin Maechler <maechler@stat.math.ethz.ch>
454 :    
455 :     * man/dpoMatrix-class.Rd: added 'corMatrix' example
456 :    
457 :     * src/dsyMatrix.[ch] (dsyMatrix_as_matrix): new 'keep_dimnames' arg
458 :     * src/dtrMatrix.[ch] (dtrMatrix_as_matrix): ditto
459 :     * src/init.c, R/dsyMatrix.R, R/dtrMatrix.R, R/lgTMatrix.R: ditto
460 :    
461 :     * R/lsparseMatrix.R: bug fix in "all" method
462 :     * R/Ops.R (.do.Logic.lsparse): "|" bug in borderline case
463 :    
464 :     * R/dsyMatrix.R (coerce->dsTMatrix): (i,j) slots should *not* have names
465 :     * R/ngTMatrix.R (coerce->ngTMatrix): ditto;
466 :     + matrix |-> nMatrix coercion
467 :     * R/pMatrix.R: + setAs() to dMatrix and from nMatrix
468 :     * man/pMatrix-class.Rd: ditto
469 :    
470 :     * R/Matrix.R (Summary): method for non-dMatrix
471 :    
472 :     * tests/Class+Meth.R (extraValid): new check about "dirty" slots
473 :     * tests/Class+Meth.R (tstMatrixClass): test norm(.);
474 :     test all Summary methods.
475 :    
476 :     2007-07-16 Martin Maechler <maechler@stat.math.ethz.ch>
477 :    
478 :     * R/dgeMatrix.R (norm, rcond): methods for 'matrix'
479 :    
480 :     2007-07-14 Martin Maechler <maechler@stat.math.ethz.ch>
481 :    
482 :     * R/sparseMatrix.R (norm): simple methods for sparseMatrix
483 :    
484 :     * R/pMatrix.R (t?crossprod): methods for pMatrix
485 :    
486 : bates 1987 2007-07-10 Douglas Bates <bates@stat.wisc.edu>
487 :    
488 :     * src/dgeMatrix.c (dgeMatrix_colsums): Get the logic straight.
489 :    
490 : bates 1975 2007-07-09 20:45 Douglas Bates <bates@stat.wisc.edu>
491 :    
492 :     * [r4579] src/dgeMatrix.c: Untangle horrible code in dgeMatrix_colsums
493 : maechler 2005 trying to fix a subtle bug - which has been somewhere else.
494 : bates 1975
495 :     2007-07-09 19:43 Martin Maechler <maechler@stat.math.ethz.ch>
496 :    
497 :     * [r4578] src/dgeMatrix.c: "cleaned" dgeMatrix_colsums() - but did not
498 :     solve the bug
499 :    
500 : maechler 1968 2007-07-08 Martin Maechler <maechler@stat.math.ethz.ch>
501 : bates 1964
502 : maechler 1968 * src/dgCMatrix.c (compressed_to_TMatrix):
503 :    
504 :     2007-07-07 Martin Maechler <maechler@stat.math.ethz.ch>
505 :    
506 :     * src/Csparse.c (Rsparse_validate): new, to have some validity
507 :     checking for RsparseMatrix
508 :     * src/dgCMatrix.c (xRMatrix_validate): ditto
509 :     * src/dtCMatrix.c (tRMatrix_validate): ditto
510 :    
511 :     2007-07-07 Douglas Bates <bates@stat.wisc.edu>
512 :    
513 : bates 1964 * [r4567] R/AllClass.R: Slots already in RsparseMatrix were redefined in
514 :     lgRMatrix
515 :     * [r4568] DESCRIPTION: Prepare for bug-fix release
516 : bates 1966 * [r4570] src/CHOLMOD/Check/cholmod_write.c: Include cholmod_matrixops.h
517 :     for declaration of cholmod_symmetry
518 : maechler 1968
519 : maechler 1961 2007-07-06 Martin Maechler <maechler@stat.math.ethz.ch>
520 :    
521 :     * DESCRIPTION (Version): 0.999375 merged into the trunk; ready for
522 :     release.
523 :    
524 : maechler 1960 2007-07-06 14:11 Douglas Bates <bates@stat.wisc.edu>
525 :    
526 :     * [r4559] src/iohb.c, src/iohb.h: Remove Harwell-Boeing input/output
527 :     functions - no longer used
528 :     * [r4560] src/HBMM.c, src/Mutils.c, src/dgTMatrix.c, src/dgeMatrix.c,
529 :     src/dspMatrix.c, src/dsyMatrix.c, src/dtCMatrix.c,
530 :     src/factorizations.c, src/sparseQR.c: Replace most calls to Calloc by
531 :     Alloca
532 :    
533 :     2007-07-06 13:14 Martin Maechler <maechler@stat.math.ethz.ch>
534 :    
535 :     * [r4558] inst/doc/Comparisons.Rnw, src/CHMfactor.c, src/Csparse.c,
536 :     src/Tsparse.c, src/chm_common.c, src/chm_common.h, src/dense.c,
537 :     src/dgCMatrix.c, src/dsCMatrix.c, src/dtTMatrix.c, src/sparseQR.c,
538 :     src/t_gCMatrix_colSums.c: more R_CheckStack()s
539 :    
540 :     2007-07-05 18:12 Douglas Bates <bates@stat.wisc.edu>
541 :    
542 :     * [r4550] inst/include/Matrix.h: Add the macro N_AS_CHM_DN to "alloca"
543 :     the required amount of memory then call M_numeric_as_chm_dense.
544 :     * [r4556] src/Mutils.h, src/dgCMatrix.c: Define and use the Alloca macro
545 :     (like Calloc but calling alloca)
546 :    
547 : maechler 1947 2007-07-05 Martin Maechler <maechler@stat.math.ethz.ch>
548 :    
549 :     * R/sparseMatrix.R (printSpMatrix): renamed from prSpMatrix()
550 :     and extended with more sophisticated 'col.names' option.
551 :     * NAMESPACE: export printSparseMatrix()
552 :     * man/printSpMatrix.Rd: document, incl. examples
553 :    
554 : maechler 1960 2007-07-04 16:21 Douglas Bates <bates@stat.wisc.edu>
555 :    
556 :     * [r4543] src/cs_utils.c, src/cs_utils.h, src/dgCMatrix.c,
557 :     src/dtCMatrix.c, src/sparseQR.c: CSP typedef for *cs and macro
558 :     AS_CSP. API change - pass the empty structure to Matrix_as_cs.
559 :    
560 : maechler 1945 2007-07-04 Martin Maechler <maechler@stat.math.ethz.ch>
561 :    
562 :     * DESCRIPTION (Version): 0.99875-4
563 :    
564 :     * tests/Class+Meth.R (tstMatrixClass): add dimnames, and hence test
565 :     some dimnames perservation.
566 :    
567 :     * R/dsTMatrix.R (t-method): keep dimnames
568 :     * R/dtTMatrix.R: ditto
569 :    
570 :     * R/sparseMatrix.R (prSpMatrix): print colnames when non-trivial
571 :     and ncol(.) < 10
572 :    
573 :     * src/cs_utils.c: drop check_class() and use Matrix_check_class()
574 :     from Mutils.h
575 :    
576 :     * src/lgCMatrix.c ([ln]csc_to_matrix): no longer lose dimnames,
577 :     e.g. in as(<ngCMatrix>, "matrix")
578 :    
579 : maechler 1960 2007-07-01 13:27 Douglas Bates <bates@stat.wisc.edu>
580 :    
581 :     * [r4529] .: Create a branch for the API changes from the 0.99875
582 :     series to the 0.999375 series
583 :     * [r4530] DESCRIPTION, inst/include/Matrix.h,
584 :     inst/include/Matrix_stubs.c, src/CHMfactor.c, src/Csparse.c,
585 :     src/Mutils.h, src/Tsparse.c, src/chm_common.c, src/chm_common.h,
586 :     src/dense.c, src/dgCMatrix.c, src/dsCMatrix.c, src/dtTMatrix.c,
587 :     src/t_gCMatrix_colSums.c: API change - pass the empty structure to the
588 :     as_cholmod_x functions
589 :    
590 :     2007-06-30 09:05 Martin Maechler <maechler@stat.math.ethz.ch>
591 :    
592 :     * [r4527] trunk/Matrix/DESCRIPTION, trunk/Matrix/NAMESPACE,
593 :     trunk/Matrix/inst/doc/Comparisons.Rnw: add session- and hardware-info
594 :     to Comparisons
595 :    
596 :     >>>>>>> .merge-right.r4561
597 : maechler 1932 2007-06-29 Martin Maechler <maechler@stat.math.ethz.ch>
598 :    
599 :     * DESCRIPTION (Version): 0.99875-3 ready to be released.
600 :    
601 :     * R/sparseMatrix.R (spMatrix): make spMatrix(3,4) working
602 :    
603 :     * R/AllGeneric.R: set "Math" (and "Math2") group generics in a way
604 :     that should also work in a future version of R.
605 :    
606 : maechler 1922 2007-06-21 Martin Maechler <maechler@stat.math.ethz.ch>
607 :    
608 :     * NAMESPACE, R/AllClass.R: "xsparseVector" class union.
609 :    
610 :     * R/sparseVector.R: more *sparseVector coercions, notably for
611 :     non - double ones.
612 :    
613 : maechler 1911 2007-06-19 Martin Maechler <maechler@stat.math.ethz.ch>
614 :    
615 :     * R/colSums.R: new file for all (col|row)(Sums|Means) methods,
616 :     notably the new ones building on the new .Call(.)s:
617 :    
618 :     * src/dgCMatrix.c (DEF_gCMatrix_COLSUMS): use to define
619 :     all 4 of [dlin]gCMatrix_colSums().
620 :    
621 : bates 1909 2007-06-18 16:12 Douglas Bates <bates@stat.wisc.edu>
622 :    
623 :     * [r4472] src/Syms.h, src/init.c: Added Matrix_lengthSym
624 :     * [r4473] src/dgCMatrix.c: Modified dgCMatrix_colSums for sparseVector
625 :     result
626 : maechler 1911
627 : maechler 1903 2007-06-16 Martin Maechler <maechler@stat.math.ethz.ch>
628 :    
629 : maechler 1904 * R/kronecker.R: fix typo (could lead to inf.recursion)
630 :     * test/simple.R: testing that
631 :    
632 : maechler 1903 * R/sparseMatrix.R (prSpMatrix): change to be used as print()
633 : maechler 1922 method as well (which can have arguments, show() can't).
634 : maechler 1903
635 : bates 1902 2007-06-16 15:52 Douglas Bates <bates@stat.wisc.edu>
636 :    
637 :     * [r4466] R/dgCMatrix.R, src/dgCMatrix.c, src/dgCMatrix.h, src/init.c:
638 :     added dgCMatrix_colSums for [col,row][Sums,Means]
639 :    
640 : bates 1899 2007-06-15 23:15 Douglas Bates <bates@stat.wisc.edu>
641 : bates 1897
642 :     * [r4460] R/sparseMatrix.R, man/dgCMatrix-class.Rd, src/dgCMatrix.c,
643 :     src/dgCMatrix.h, src/init.c: added lm.fit.sparse (unexported),
644 :     coercion of "factor" to "dgCMatrix" and dgCMatrix_cholsol
645 :     * [r4461] R/AllClass.R, man/sparseMatrix-class.Rd: draft "indicators"
646 :     class
647 : bates 1899 * [r4463] R/sparseMatrix.R, man/dgCMatrix-class.Rd,
648 :     man/sparseMatrix-class.Rd: Don't need an "indicators" class - use the
649 :     row names to store the levels - duh! Added an example.
650 : maechler 1903
651 : maechler 1893 2007-06-14 Martin Maechler <maechler@stat.math.ethz.ch>
652 :    
653 :     * src/Csparse.c (Csparse_validate): check for *repeated* entries
654 :     thanks to example from Christian Buchta; with a test here:
655 :     * tests/simple.R:
656 :    
657 : maechler 1886 2007-06-07 Martin Maechler <maechler@stat.math.ethz.ch>
658 :    
659 :     * R/Auxiliaries.R (callGeneric): another fix, needed for some cases
660 :     of colSums(*, sparseResult = TRUE)
661 :    
662 : maechler 1883 2007-06-06 Martin Maechler <maechler@stat.math.ethz.ch>
663 :    
664 :     * R/lsparseMatrix.R, R/ldenseMatrix.R (all, any): change default to
665 :     'na.rm = FALSE' as "everywhere" else in R.
666 :    
667 : bates 1877 2007-06-05 Douglas Bates <bates@stat.wisc.edu>
668 :    
669 : bates 1878 * [r4421] src/CSparse_install.sh: Modify for new organization of
670 : maechler 1883 CSparse package
671 : bates 1877 * [r4425] src/UFsparse_download.sh: Update to version 3.0.0 of
672 :     SuiteSparse
673 :     * [r4426] src/Makefile: add ./UFconfig to the include path for
674 :     compilation
675 : maechler 1883 * [r4427] src/cs.[ch]: update to CSparse version 2.2.0
676 :     * [r4428] inst/doc/UFsparse/* src/{AMD,CHOLMOD,COLAMD}/*
677 :     src/UFconfig/UFconfig.h: Update to version 3.0.0 of SuiteSparse
678 :    
679 : maechler 1870 2007-06-05 Martin Maechler <maechler@stat.math.ethz.ch>
680 :    
681 :     * R/Auxiliaries.R (emptyColnames): + argument msg.if.not.empty, used in
682 :     * R/sparseMatrix.R (prSpMatrix): now gives a message about
683 :     suppressed column names.
684 :    
685 : bates 1868 2007-06-04 17:13 Douglas Bates <bates@stat.wisc.edu>
686 :    
687 :     * [r4418] src/Csparse.c, src/HBMM.c, src/Mutils.c, src/Mutils.h,
688 :     src/Tsparse.c, src/chm_common.c, src/chm_common.h, src/dgCMatrix.c,
689 :     src/dgeMatrix.c, src/dpoMatrix.c, src/dpoMatrix.h, src/dppMatrix.c,
690 :     src/dppMatrix.h, src/dsCMatrix.c, src/dspMatrix.c, src/dspMatrix.h,
691 :     src/dsyMatrix.c, src/dsyMatrix.h, src/dtpMatrix.c, src/dtrMatrix.c:
692 :     Remove warnings after change to const char* CHAR
693 :    
694 :     2007-06-04 17:11 Douglas Bates <bates@stat.wisc.edu>
695 :    
696 :     * [r4417] inst/include/Matrix_stubs.c, inst/include/cholmod.h: Corrected
697 :     type of M_cholmod_ssmult
698 :    
699 : bates 1863 2007-06-03 14:42 Douglas Bates <bates@stat.wisc.edu>
700 :    
701 :     * [r4412] inst/include/Matrix_stubs.c, inst/include/cholmod.h,
702 :     src/init.c: Yet another cholmod export - cholmod_ssmult
703 :    
704 : maechler 1855 2007-05-23 Martin Maechler <maechler@stat.math.ethz.ch>
705 :    
706 :     * NAMESPACE: exported drop0(), since
707 :     * man/drop0.Rd: I have seen several cases, I really wanted to use
708 :     it, so our users may want too.
709 :    
710 :     2007-05-22 Martin Maechler <maechler@stat.math.ethz.ch>
711 :    
712 :     * man/colSums.Rd: separately document colSums() etc, since these
713 :     have the extra argument 'sparseResult'.
714 :    
715 : maechler 1852 2007-05-21 Martin Maechler <maechler@stat.math.ethz.ch>
716 :    
717 :     * R/sparseMatrix.R (spMatrix): utility (T)sparse Matrix constructor;
718 :     * man/spMatrix.Rd: docu., including examples
719 :    
720 :     * R/Auxiliaries.R (sp.colMeans): etc, using a patched callGeneric(),
721 :     in order to make colMeans() etc fast *and* correct.
722 :     * R/sparseVector.R (replSPvec): "[<-" functionality for
723 :     sparseVectors; tested in
724 :     * tests/simple.R:
725 :    
726 :     2007-05-19 Martin Maechler <maechler@stat.math.ethz.ch>
727 :    
728 :     * R/sparseMatrix.R (print.sparseSummary): and summary() method for
729 :     (very) sparse Matrices; output similar to Matlab's print().
730 :    
731 : bates 1847 2007-05-17 Douglas Bates <bates@stat.wisc.edu>
732 :    
733 :     * src/HBMM.c (Matrix_writeMatrixMarket): Write 1-based, not
734 :     0-based, indices (Jose Quesada <quesada@gmail.com>).
735 :    
736 : bates 1844 2007-05-16 Douglas Bates <bates@stat.wisc.edu>
737 :    
738 :     * R/CHMfactor.R: Added solve methods for a CHMfactor object.
739 :    
740 : maechler 1845 2007-05-16 Martin Maechler <maechler@stat.math.ethz.ch>
741 :    
742 :     * R/Auxiliaries.R (sparsapply): new utility, much faster than
743 :     tapply1() for large sparse matrices.
744 :    
745 :     2007-05-15 Martin Maechler <maechler@stat.math.ethz.ch>
746 :    
747 :     * R/Matrix.R (dim<-): reshape now via sparseVector.
748 :    
749 :     * R/sparseVector.R: methods and function for
750 :     * R/AllClass.R: new "sparseVector" class and daughters.
751 :     * NAMESPACE: export new classes
752 :    
753 : maechler 1837 2007-05-14 Martin Maechler <maechler@stat.math.ethz.ch>
754 :    
755 :     * DESCRIPTION (Version): 0.99875-1
756 :     * src/Makefile.win: also remove Lapack code from here (cf. 04-25).
757 :    
758 : maechler 1834 2007-05-11 Martin Maechler <maechler@stat.math.ethz.ch>
759 :    
760 :     * R/Tsparse.R ([, Tsparse): fix last case: *duplicated*, symmetric
761 :     indexing
762 :     * tests/indexing.R: test set for that.
763 :    
764 : maechler 1833 2007-05-08 Martin Maechler <maechler@stat.math.ethz.ch>
765 :    
766 :     * R/Tsparse.R (replTmat): fix the case of *duplicated* index
767 :     entries.
768 :     * tests/indexing.R(out): add regression test for it
769 :    
770 :     2007-04-30 Martin Maechler <maechler@stat.math.ethz.ch>
771 :    
772 :     * R/(l(dense|sparse))?Matrix.R (!): use 'x', not 'e1' as argument
773 :     name for "!" method definitions.
774 :    
775 : maechler 1829 2007-04-26 Martin Maechler <maechler@stat.math.ethz.ch>
776 :    
777 :     * R/Tsparse.R (intI): new utility, used for "[" :
778 :     Cleanup up there, and fixes for duplicated indices - more TODO!
779 :    
780 :     * tests/indexing.R(out): more tests
781 :    
782 : bates 1827 2007-04-25 Douglas Bates <bates@stat.wisc.edu>
783 :    
784 :     * DESCRIPTION,src/Makefile: require R>= 2.5.0 and remove Lapack
785 :     code that is now part of the R Lapack library.
786 : maechler 1829
787 : bates 1827 * src/init.c,inst/include/{Matrix_stubs.c,cholmod.h}:export
788 :     cholmod_factorize_p (used in lme4 for GLMMs and NLMMs).
789 :    
790 : maechler 1829 2007-04-21 Martin Maechler <maechler@stat.math.ethz.ch>
791 :    
792 :     * R/Matrix.R (image): method for all Matrices, not just sparse ones.
793 :    
794 :     2007-04-17 Martin Maechler <maechler@stat.math.ethz.ch>
795 :    
796 :     * R/Auxiliaries.R (tapply1): unname(.) -> colSums() etc don't end
797 :     up with extraneous names '0'...'<n-1>'
798 :    
799 : maechler 1825 2007-04-12 Martin Maechler <maechler@stat.math.ethz.ch>
800 :    
801 :     * R/dgTMatrix.R (mat2dgT): care about NAs
802 :    
803 :     2007-04-11 Martin Maechler <maechler@stat.math.ethz.ch>
804 :    
805 :     * R/kronecker.R: triangularity preserving methods
806 :    
807 : maechler 1803 2007-03-27 Martin Maechler <maechler@stat.math.ethz.ch>
808 :    
809 :     * R/kronecker.R: new file collecting kronecker() methods in one
810 :     place. Goal: become much faster!
811 :    
812 : maechler 1799 2007-03-23 Martin Maechler <maechler@stat.math.ethz.ch>
813 :    
814 :     * src/dtCMatrix.c (dtCMatrix_solve): use the new code from Kasper
815 :     Kristensen based cs_spsolve() instead of _lsolve & _usolve which
816 :     can be much faster.
817 :    
818 :     * tests/matprod.R: add regression tests for these (upper & lower).
819 :    
820 :     2007-03-19 Martin Maechler <maechler@stat.math.ethz.ch>
821 :    
822 :     * R/Matrix.R (diff): method for our Matrices.
823 :    
824 :     * R/sparseMatrix.R (isDiagonal): check dim()!
825 :    
826 :     2007-03-17 Martin Maechler <maechler@stat.math.ethz.ch>
827 :    
828 :     * R/Matrix.R (dim<-): new method for "reshape()" built on a
829 :     proposal from Tamas Papp.
830 :    
831 :     2007-03-16 Martin Maechler <maechler@stat.math.ethz.ch>
832 :    
833 :     * R/AllGeneric.R: remove all if(!isGeneric(.)) clauses
834 :    
835 :     * R/zzz.R (.onLoad, .onUnload): do *not* leave bind_activation(TRUE);
836 : maechler 1803 rather define and export cBind() and rBind() only.
837 :     --> useRs *must* change code that used to have cbind()/rbind() !!
838 : maechler 1799
839 : maechler 1803 * R/bind.R: change tests from cbind() to cBind() and similarly to rBind()
840 :     * R/bind.Rout.save: ditto
841 : maechler 1799
842 : bates 1787 2007-02-16 Douglas Bates <bates@r-project.org>
843 :    
844 :     * DESCRIPTION (Date, Version): 0.9975-11 with new date
845 :     * src/dgCMatrix.c (R_to_CMatrix, compressed_to_TMatrix): remove
846 :     const modifier on declaration of the array 'valid'
847 :    
848 : bates 1786 2007-02-12 Douglas Bates <bates@stat.wisc.edu>
849 :    
850 :     * R/CHMfactor.R: Add image method (coercion to sparseMatrix).
851 :    
852 : maechler 1765 2007-02-05 Martin Maechler <maechler@stat.math.ethz.ch>
853 :    
854 : maechler 1768 * DESCRIPTION (Date, Version): 0.9975-10 with new date.
855 :    
856 : maechler 1767 * R/Ops.R (Arith): make sure Csparse o Csparse also works for e.g. ntCMatrix
857 :     * tests/simple.R: test the above and some of these coercions:
858 :    
859 :     * R/nsparseMatrix.R: coercing "Csparse" to "lsparseMatrix";
860 :     be careful to avoid infinite recursion, using new coercions in
861 :     * R/ngCMatrix.R and nsC... and ntC...
862 :     * R/lsparseMatrix.R: ditto
863 :    
864 : maechler 1765 * R/SparseM-conv.R: more conversion, notably for triplet matrices.
865 :    
866 : maechler 1767 * src/dgCMatrix.c (R_to_C_Matrix): port Doug's fix and
867 :     * R/Rsparse.R: reactivate .Call()s
868 : maechler 1765
869 : maechler 1767 * tests/Class+Meth.R: a bit more on actual classes
870 :    
871 :     2007-02-04 Douglas Bates <bates@stat.wisc.edu>
872 :    
873 :     * src/dgCMatrix.c (compressed_to_TMatrix): fix memory bug using strdup()
874 :    
875 : maechler 1760 2007-02-03 Martin Maechler <maechler@stat.math.ethz.ch>
876 : maechler 1758
877 :     * DESCRIPTION (Version): 0.9975-10 to upload
878 :    
879 : maechler 1760 * tests/Class+Meth.R (tstMatrixClass): require coercions to
880 :     specific classes less unconditionally.
881 :    
882 :     * R/Auxiliaries.R: get rid of as_Tsparse() and as_Rsparse()
883 :    
884 :     * R/Tsparse.R (triu): etc, use as(*, "TsparseMatrix") instead of as_Tsparse()
885 :    
886 :     * R/Rsparse.R (.R.2.T): R-level workaround using compressed_to_TMatrix.
887 : maechler 1758 * R/Rsparse.R (.R.2.C): R-level workaround since C-level
888 :     R_to_CMatrix segfaults on one platform.
889 : maechler 1760 Eliminate most coercion method to *specific* classes, and replace
890 :     with virtual classes coercions.
891 : maechler 1758
892 : maechler 1760
893 : maechler 1758 2007-02-01 Martin Maechler <maechler@stat.math.ethz.ch>
894 :    
895 :     * src/init.c: export the CHM...._validate() placeholders, since
896 :     they *are* called.
897 :    
898 : maechler 1760 * tests/Class+Meth.R (classCanCoerce): and starting to test
899 : maechler 1758 all as(<from>, <to>)
900 :    
901 : maechler 1751 2007-01-30 Martin Maechler <maechler@stat.math.ethz.ch>
902 :    
903 :     * R/Tsparse.R ([): more care when subsetting triangular Tsparse
904 :     * tests/indexing.R: tested now
905 :     * tests/indexing.Rout.save: updated
906 :    
907 :     * src/Csparse.c (Csparse_to_dense): use Rkind = -1 for PATTERN to
908 :     * src/chm_common.c (chm_dense_to_SEXP): return "ngeMatrix" when
909 :     appropriate.
910 :    
911 :     * NAMESPACE: export a trivial
912 :     * R/Matrix.R: drop() Matrix-method
913 :    
914 :     * R/AllClass.R: moved all prototypes to virtual super classes.
915 :    
916 :     * R/Rsparse.R: many more coercions to have less exceptions in
917 :     * tests/Class+Meth.R:
918 :    
919 :     * R/Ops.R (Compare): tweak for case with NA
920 :     * tests/simpl.R: hence another 'FIXME' eliminated
921 :    
922 : maechler 1747 2007-01-29 Martin Maechler <maechler@stat.math.ethz.ch>
923 :    
924 : maechler 1748 * R/diagMatrix.R (solve): the obvious methods for diagonalMatrix
925 :     objects.
926 :    
927 : maechler 1747 * tests/Class+Meth.R (tstMatrixClass): now testing diag(), nnzero(),
928 :     and more of "!", "&", "|", all, any; coercions
929 :    
930 :     * R/Rsparse.R: many coercions (which enable quite a few other
931 :     methods), thanks to enhancements in
932 :     * src/dgCMatrix.c (R_to_CMatrix): new, and
933 :     * src/dgCMatrix.c (compressed_to_TMatrix): now for (d,l,n) ,
934 :     symmetric & triangular and ..RMatrix objects.
935 :    
936 :     * src/TMatrix_as.c (Matrix_T_as_DENSE,Matrix_T_as_GENERAL):
937 :     renamed file from src/dsTMatrix.c;
938 :     now dealing with symmetric and triangular Tsparse coercions, both
939 :     to dense and general.
940 :    
941 :     2007-01-27 Martin Maechler <maechler@stat.math.ethz.ch>
942 :    
943 :     * src/dsTMatrix.c: has now "l" and "n" methods besides the "d" ones.
944 :    
945 :     * R/Ops.R (Arith): <dgCMatrix> o <numeric> now remains sparse
946 :     where sensible when the <numeric> is of length > 1.
947 :    
948 :     2007-01-26 Martin Maechler <maechler@stat.math.ethz.ch>
949 :    
950 :     * R/Matrix.R ([<-): for M[] <- value: fix length
951 :    
952 :     2007-01-25 Martin Maechler <maechler@stat.math.ethz.ch>
953 :    
954 :     * R/Auxiliaries.R (n2l_Matrix): new, to be used in
955 :     * R/ndenseMatrix.R: new coercions n* -> l*
956 :    
957 : maechler 1738 2007-01-22 Martin Maechler <maechler@stat.math.ethz.ch>
958 :    
959 :     * R/triangularMatrix.R: new file; simple triu() and tril() methods.
960 :    
961 :     * R/Ops.R ("Logic"): and other "Ops", many updates
962 :    
963 :     2007-01-18 Martin Maechler <maechler@stat.math.ethz.ch>
964 :    
965 :     * src/Mutils.h (SET_DimNames): new utility
966 :    
967 :     * R/Auxiliaries.R (nnzero): improved and now exported via
968 :    
969 :     * NAMESPACE: + nnzero(); length() == prod(dim(.)) method for all "Matrix" objects
970 :    
971 : maechler 1725 2007-01-17 Martin Maechler <maechler@stat.math.ethz.ch>
972 :    
973 :     * R/diagMatrix.R (!): fix typo.
974 :    
975 :     2007-01-16 Martin Maechler <maechler@stat.math.ethz.ch>
976 :    
977 :     * R/Auxiliaries.R (as_Csparse): and quite a few others:
978 :     allow to pass class definition --> speedup
979 :     * R/sparseMatrix.R: apply the above
980 :    
981 :     * R/Csparse.R: coercion Csparse* to dense* now preserves shape properties.
982 :    
983 :     * src/Mutils.h (mMatrix_as_geMatrix): new, based on
984 :     * src/Mutils.c (dup_mMatrix_as_geMatrix): new; generalization of
985 :     old dup_mMatrix_as_dgeMatrix), eliminating a long-standing "FIXME".
986 :    
987 :     * src/dense.c (dense_to_Csparse): use new mMatrix_as_geMatrix()
988 :    
989 :     * R/denseMatrix.R (.dense2C): based on dense_to_Csparse: name it,
990 :     and use it for "sparse*" as well, since it's faster than the
991 :     as_Csparse(.) way.
992 :    
993 :     2007-01-15 Martin Maechler <maechler@stat.math.ethz.ch>
994 :    
995 :     * R/Ops.R ("Logic"): more methods, notably an <lgC> o <lgC> one.
996 :    
997 : maechler 1724 2007-01-12 Martin Maechler <maechler@stat.math.ethz.ch>
998 :    
999 :     * R/Tsparse.R (.TM.repl.i.2col): new internal function to be used
1000 :     as method for M[ ij ] <- v
1001 :     * R/Csparse.R:: go via Tsparse for "M[ij] <- v"
1002 :    
1003 :     * R/Ops.R: "Compare" for (C|R)sparse: need pointer slot for all
1004 :     FALSE answer
1005 :    
1006 :     * R/Csparse.R (replCmat): fix the "all non-zero" case with reordering
1007 :     * tests/indexing.R: test it, and some of the above
1008 :    
1009 :     2007-01-05 Martin Maechler <maechler@stat.math.ethz.ch>
1010 :    
1011 :     * R/Auxiliaries.R (is_duplicatedT): new utility
1012 :    
1013 : bates 1716 2007-01-05 Douglas Bates <bates@stat.wisc.edu>
1014 :    
1015 :     * src/init.c (R_init_Matrix): export cholmod_scale
1016 :    
1017 : maechler 1724 2006-12-30 Martin Maechler <maechler@stat.math.ethz.ch>
1018 :    
1019 :     * R/zzz.R (tmp): for R >= 2.5.0, extend formals of our
1020 :     base::as.matrix to (x, ...)
1021 :    
1022 : maechler 1714 2006-12-28 Martin Maechler <maechler@stat.math.ethz.ch>
1023 :    
1024 :     * R/Ops.R ("Arith" etc): move almost all "Ops" methods to new R
1025 :     file; start using "Logic", hence
1026 :    
1027 :     * DESCRIPTION (Depends): R >= 2.4.1 (since we want "Logic")
1028 :     * NAMESPACE: import and export "Logic"
1029 :    
1030 :     2006-12-27 Martin Maechler <maechler@stat.math.ethz.ch>
1031 :    
1032 :     * src/zpotfr.f and dependencies: use LAPACK 3.1 version
1033 :     only needed previously to R version 2.5.0.
1034 : maechler 1724
1035 : maechler 1710 2006-12-26 Martin Maechler <maechler@stat.math.ethz.ch>
1036 :    
1037 :     * DESCRIPTION (Date, Version): 0.9975-8, ready for release
1038 :    
1039 :     * R/Tsparse.R (replTmat): fix subassignment of triangular
1040 :     * R/Csparse.R (replCmat): ditto
1041 :     * tests/indexing.R: more tests, incl the above fix
1042 :    
1043 :     2006-12-23 Martin Maechler <maechler@stat.math.ethz.ch>
1044 :    
1045 :     * R/Auxiliaries.R (drop0): extend for non CSparse
1046 :     * R/Auxiliaries.R (diagU2N): should work for all sparseMatrix
1047 :    
1048 :     * src/Csparse.c (Csparse_to_Tsparse, Csparse_general_to_symmetric):
1049 :     use uplo correctly (!); other places: use uplo_P() macro
1050 :    
1051 :     * R/Csparse.R (replCmat): call diagU2N() when needed
1052 :     * R/Tsparse.R (replTmat): ditto
1053 :    
1054 :     * src/dtCMatrix.c (tCMatrix_validate): new
1055 :     * src/dtTMatrix.c (tTMatrix_validate): new, used in
1056 :     * R/AllClass.R: for validity of dtC, dsC, and dtT, dsT.
1057 :    
1058 :     * R/diagMatrix.R (replDiag): to use in [<-
1059 :    
1060 : maechler 1708 2006-12-22 Martin Maechler <maechler@stat.math.ethz.ch>
1061 :    
1062 :     * R/Auxiliaries.R (as_Csparse2, as_geSimpl): new functions;
1063 :     also more general diagU2N().
1064 :    
1065 :     2006-12-21 Martin Maechler <maechler@stat.math.ethz.ch>
1066 :    
1067 :     * R/bind2.R: new file for all cbind2(), rbind() methods moved here
1068 :     from R/<foo>Matrix.R files. Better diagonal & improved sparse methods.
1069 :    
1070 : maechler 1707 2006-12-20 Martin Maechler <maechler@stat.math.ethz.ch>
1071 :    
1072 :     * tests/bind.R: a few more cases
1073 :     * R/Auxiliaries.R (.M.kind): also work for atomic vectors
1074 :    
1075 :     * R/denseMatrix.R (cbind2/rbind2): moved here (and generalized) from
1076 :     * R/ddenseMatrix.R (cbind2/rbind2)
1077 :     * R/Tsparse.R (replTmat): final(?!) fix for "[<-" ..
1078 :     * tests/indexing.R
1079 :     * tests/indexing.Rout.save: updated
1080 :    
1081 :     2006-12-18 Martin Maechler <maechler@stat.math.ethz.ch>
1082 :    
1083 :     * R/Tsparse.R (replTmat): fixed a remaining "[<-" bug in
1084 :     * tests/indexing.R
1085 :    
1086 : maechler 1705 2006-12-15 Martin Maechler <maechler@stat.math.ethz.ch>
1087 :    
1088 :     * R/sparseMatrix.R (prSpMatrix): "." alignment much improved:
1089 :     align with proper position of "0", i.e., right for integers.
1090 :     argument 'align' by default is "fancy".
1091 :    
1092 :     2006-12-14 Martin Maechler <maechler@stat.math.ethz.ch>
1093 :    
1094 :     * R/sparseMatrix.R: delegate "Compare" to "Csparse.."
1095 :     * R/Csparse.R: and fix "Compare" for more cases.
1096 :     * tests/Class+Meth.R: test some of these (m == m, m != m)
1097 :    
1098 :     2006-12-13 Martin Maechler <maechler@stat.math.ethz.ch>
1099 :    
1100 :     * R/lsparseMatrix.R: all() and any() methods
1101 :     * R/ldenseMatrix.R: ditto
1102 :     * NAMESPACE, R/Matrix.R: ditto
1103 :    
1104 :     * man/all-methods.Rd: document them minimally
1105 :    
1106 :     * tests/simple.R: add a few examples for these
1107 :    
1108 : maechler 1696 2006-12-11 Martin Maechler <maechler@stat.math.ethz.ch>
1109 :    
1110 :     * R/Tsparse.R ([): fix long standing typo in symmetric case
1111 :     * man/dsCMatrix-class.Rd: add example exhibiting the above case
1112 :    
1113 : bates 1691 2006-12-10 Douglas Bates <bates@stat.wisc.edu>
1114 :    
1115 :     * src/CHMfactor.c (CHMfactor_to_sparse): change LDL factorization
1116 :     to LL before converting to a sparse matrix. (The LDL form can be
1117 :     converted to a sparse matrix but it is implicitly a unit
1118 :     triangular matrix and a diagonal matrix overwritten on the diagonal.)
1119 :    
1120 :     2006-12-09 Douglas Bates <bates@stat.wisc.edu>
1121 :    
1122 :     * src/chm_common.c (chm_factor_to_SEXP): allocate and fill the Dim slot.
1123 :    
1124 : bates 1688 2006-12-08 Douglas Bates <bates@stat.wisc.edu>
1125 :    
1126 :     * DESCRIPTION (Version): updated -> release 0.9975-7
1127 :     * src/{init.c,chm_common.c}, inst/include/*: export cholmod_analyze_p
1128 :    
1129 : maechler 1682 2006-11-30 Martin Maechler <maechler@stat.math.ethz.ch>
1130 :    
1131 :     * R/diagMatrix.R (%*%): write a direct [diag o Csparse] method
1132 :    
1133 : bates 1681 2006-11-29 Douglas Bates <bates@stat.wisc.edu>
1134 :    
1135 :     * src/dgeMatrix.c (dgeMatrix_solve): Check error code from dgetri.
1136 :     * tests/dg_Matrix.R: Add Barry Rowlingson's test of a matrix that
1137 :     is exactly singular.
1138 :    
1139 : maechler 1674 2006-11-07 Martin Maechler <maechler@stat.math.ethz.ch>
1140 :    
1141 :     * DESCRIPTION (Date): updated -> release 0.9975-6
1142 :    
1143 : maechler 1673 2006-11-06 Martin Maechler <maechler@stat.math.ethz.ch>
1144 :    
1145 :     * R/Csparse.R (replCmat): symmetric indexing of symmetric matrix
1146 :     now returns symmetric.
1147 :    
1148 :     * R/zzz.R ("diag<-"): replace "diag<-" in base for R <= 2.4.x
1149 :    
1150 :     * R/Matrix.R (.M.sub.i.2col): new, for M[ cbind(i,j) ] indexing.
1151 :     * R/Matrix.R (.M.repl.i.2col): new, for M[ cbind(i,j) ] <- value
1152 :    
1153 :     * R/Auxiliaries.R (.type.kind): added
1154 :    
1155 :     2006-11-04 Martin Maechler <maechler@stat.math.ethz.ch>
1156 :    
1157 :     * src/cs.[ch]: updated to CSparse Version 2.0.3 by simply
1158 :     running src/CSparse_install.sh
1159 :    
1160 :     * R/denseMatrix.R: "[": keep symmetric on symmetric indexing.
1161 :    
1162 : maechler 1665 2006-11-03 Martin Maechler <maechler@stat.math.ethz.ch>
1163 :    
1164 :     * src/dsCMatrix.c (dsCMatrix_Csparse_solve): new
1165 :     * R/dsCMatrix.R (solve): "fully-sparse" using the above.
1166 :    
1167 :     * R/AllClass.R: "pMatrix" now also inherits from "generalMatrix"
1168 :    
1169 :     * tests/Class+Meth.R (tstMatrixClass): now assure
1170 :     the (important in method programming) property :
1171 :    
1172 :     ###>> Every "Matrix" is either
1173 :     ###>> "general*", "symmetric*", "triangular*" or "diagonal*"
1174 :    
1175 :     (where "*" stands for "Matrix")
1176 :    
1177 :     * R/Auxiliaries.R (diagU2N): now .Call()s Csparse_diagU2N for <Csparse>
1178 :    
1179 :     * R/dMatrix.R (Compare(<dMatrix>,<dMatrix>): update and
1180 :     * tests/validObj.R: checks for "comparison"
1181 :    
1182 :     * R/sparseMatrix.R ([): improved indexing for sparse;
1183 :     trying to keep <symmetric>[ n, n] symmmetric
1184 :    
1185 :     * tests/indexing.R: indexing for logical sparse now ok
1186 :    
1187 :    
1188 : maechler 1660 2006-11-02 Martin Maechler <maechler@stat.math.ethz.ch>
1189 :    
1190 : maechler 1661 * src/Tsparse.c: use xTsparse_validate() , and hence remove
1191 :    
1192 :     * src/{ltC,lsC,lgT}Matrix.[ch]: removed
1193 :    
1194 :     2006-11-02 Martin Maechler <maechler@stat.math.ethz.ch>
1195 :    
1196 : maechler 1660 * R/AllClass.R (Matrix-class): check length of dimnames in validity.
1197 :    
1198 :     * tests/simple.R: validObject() checking the above.
1199 :    
1200 : maechler 1665 * src/dgCMatrix.c (xCMatrix_validate): new, small and simple,
1201 : maechler 1660 replacing both dgCMatrix_validate and lgCM*.
1202 :    
1203 :     * src/Csparse.c (Csparse_dense_prod, etc): do not lose dimnames;
1204 :     fix dimnames setting in other places.
1205 :     * src/chm_common.c (chm_dense_to_SEXP): now can pass dimnames
1206 :    
1207 : maechler 1659 2006-11-01 Martin Maechler <maechler@stat.math.ethz.ch>
1208 :    
1209 : maechler 1660 * R/Csparse.R,src/Csparse.c, etc: tcrossprod(<CsparseM>,<CsparseM>)
1210 :    
1211 :     * R/sparseMatrix.R (isSymmetric): drop 'factors' slot for
1212 :     symmetry test, via
1213 : maechler 1659 * R/Auxiliaries.R (.as.dgC.0.factors):
1214 :    
1215 : bates 1657 2006-11-01 Douglas Bates <bates@r-project.org>
1216 :    
1217 :     * R/Csparse.R,src/Csparse.c,tests/matprod.R,
1218 :     man/CsparseMatrix-class.Rd: crossprod(<CsparseMatrix>,
1219 :     <CsparseMatrix>) added
1220 :    
1221 : maechler 1655 2006-10-30 Martin Maechler <maechler@stat.math.ethz.ch>
1222 :    
1223 :     * tests/matprod.R: add a variation of Harri's example
1224 :    
1225 :     * R/dsparseMatrix.R: fix crossprod(<dsparse>, <dge>) to *not*
1226 :     recursive infinitely.
1227 :    
1228 :     * R/dgCMatrix.R: + solve(<sparse>, <sparse>)
1229 :    
1230 :     * tests/indexing.R: add test for the "<" bug fixed 10-27 in R/dMatrix.R
1231 :    
1232 :     2006-10-28 Martin Maechler <maechler@stat.math.ethz.ch>
1233 :    
1234 :     * tests/Class+Meth.R (tstMatrixClass): more: use non-trivial
1235 :     matrix if possible; test m+m == 2*m; now test dgRMatrix.
1236 :     * R/dgRMatrix.R (.to.dgR): a few more coercions, in order to
1237 :     satisfy the above test.
1238 :    
1239 : maechler 1654 2006-10-27 Martin Maechler <maechler@stat.math.ethz.ch>
1240 :    
1241 : maechler 1655 * R/Matrix.R (Ops): <Matrix> o <matrix> method added
1242 :    
1243 : maechler 1654 * R/dgCMatrix.R: solve(a, b="missing") based on
1244 :     * src/dgCMatrix.c (dgCMatrix_matrix_solve): extend to work with
1245 :     RHS = NULL.
1246 :    
1247 :     * R/diagMatrix.R (diagdiagprod): extend %*% etc to ldiMatrix;
1248 :     add more (needed) [t]crossprod() methods.
1249 :    
1250 :     * man/ddiMatrix-class.Rd: more info, notably on 'diag'
1251 :    
1252 :     * R/Auxiliaries.R (as_CspClass): cleanup
1253 :     (drop0): internal utility for "Csparse_drop(*, 0)"
1254 :     (.bail.out.2): encourage active feedback
1255 :    
1256 :     2006-10-26 Martin Maechler <maechler@stat.math.ethz.ch>
1257 :    
1258 :     * R/dMatrix.R(Compare): new(), then slots [no validity check]
1259 :    
1260 :     * src/Csparse.c (Csparse_validate): fixed (and more efficient in
1261 :     non-valid or 'sorted' case).
1262 :    
1263 :     * R/dsparseMatrix.R: add "chol" method.
1264 :     * R/ddenseMatrix.R: ditto
1265 :    
1266 :     * R/diagMatrix.R (Ops): group methods for <diagonal> o <sparse>
1267 :     * NAMESPACE (Ops)
1268 :     * R/diagMatrix.R (diag2T): simple utility used "higher level"
1269 :     coercion; deprecating direct lower level coercions.
1270 :    
1271 :     * R/*.R (seq): use seq_len() and seq_along() where possible.
1272 :    
1273 :    
1274 : maechler 1647 2006-10-23 Martin Maechler <maechler@stat.math.ethz.ch>
1275 :    
1276 :     * DESCRIPTION (Version): 0.9975-5 ready for release
1277 :    
1278 : bates 1646 2006-10-20 Douglas Bates <bates@stat.wisc.edu>
1279 :    
1280 :     * src/init.c (R_init_Matrix): export more cholmod CCallable functions.
1281 :    
1282 : maechler 1642 2006-10-20 Martin Maechler <maechler@stat.math.ethz.ch>
1283 :    
1284 :     * R/AllClass.R (corMatrix): add 'validity' check;
1285 :     comment out unused "LDL" class definition
1286 :     * NAMESPACE: mention, but do not export "LDL" class
1287 :     * R/corMatrix.R: new (simple), needed for R-devel with
1288 :     * tests/Class+Meth.R (tstMatrixClass): 1 exception for corMatrix
1289 :     coerce and t() exceptions for all 5 'Mat.MatFact' classes.
1290 :    
1291 : bates 1641 2006-10-19 Douglas Bates <bates@stat.wisc.edu>
1292 :    
1293 :     * src/chm_common.h: Add R_cholmod_start to initialize cholmod to
1294 :     use Rprintf and R's error handling.
1295 :    
1296 : maechler 1635 2006-10-17 Martin Maechler <maechler@stat.math.ethz.ch>
1297 :    
1298 :     * R/diagMatrix.R (%*%): rep(*, each = .) in Matrix %*% diagonal.
1299 :     * tests/matprod.R: add tests for the bug fixed.
1300 :    
1301 : bates 1624 2006-10-11 Douglas Bates <bates@stat.wisc.edu>
1302 :    
1303 :     * src/HBMM.[ch]: remove HarwellBoeing format for writing.
1304 :     * src/SOURCES_C.mkf (SOURCES_C): no longer compile iohb.c
1305 :    
1306 :     2006-10-06 Douglas Bates <bates@stat.wisc.edu>
1307 :    
1308 : bates 1629 * R/d[gs]CMatrix.R: deprecate the writeHB function. Use writeMM instead.
1309 : bates 1624
1310 : maechler 1618 2006-10-06 Martin Maechler <maechler@stat.math.ethz.ch>
1311 :    
1312 :     * DESCRIPTION (Version): 0.9975-3
1313 :    
1314 :     * R/diagMatrix.R (bdiag): new function constructing block diagonal
1315 :     (sparse) matrices.
1316 :     * man/bdiag.Rd: docu + examples
1317 :    
1318 : maechler 1619 * R/Csparse.R (replCmat): calling new Csparse_drop() now.
1319 :    
1320 : maechler 1618 * src/Csparse.c (Csparse_general_to_symmetric, Csparse_drop): new functions
1321 :     * R/lsCMatrix.R: three more coercions to lsC (thanks to the above)
1322 :    
1323 :     * R/diagMatrix.R (Diagonal): '[<-' method for diag.matrices such
1324 :     that result is sparse or diagonal (and not dense).
1325 :    
1326 :     * man/Subassign-methods.Rd: fix examples
1327 :    
1328 :     * R/Matrix.R (Matrix): Matrix(0, *) or Matrix(*, sparse=TRUE)
1329 :     should always return a sparse (and not sometimes a diagonal) matrix.
1330 :    
1331 : maechler 1615 2006-10-05 Martin Maechler <maechler@stat.math.ethz.ch>
1332 :    
1333 :     * R/Matrix.R ([<-): also for value "Matrix" or "matrix"
1334 :    
1335 : bates 1613 2006-10-04 Douglas Bates <bates@stat.wisc.edu>
1336 :    
1337 :     * DESCRIPTION (Version): 0.9975-2
1338 : maechler 1615
1339 : bates 1613 * inst/include/Matrix_stubs.c (M_cholmod_sparse_to_triplet): export more symbols
1340 :    
1341 : bates 1611 2006-10-02 Douglas Bates <bates@R-project.org>
1342 :    
1343 :     * tests/dg_Matrix.R: Simplify test taking into account new code.
1344 :    
1345 : maechler 1599 2006-09-29 Martin Maechler <maechler@stat.math.ethz.ch>
1346 :    
1347 : maechler 1600 * R/Csparse.R (replCmat): improve for missing i / j in non-simple cases
1348 :    
1349 : maechler 1599 * R/lsTMatrix.R: new files w/ missing methods
1350 :     * R/nsTMatrix.R: " 'for completeness'
1351 :    
1352 :     * tests/Class+Meth.R: a bit less 'not.ok.classes'
1353 :    
1354 :     * R/Tsparse.R (t): generalized "t" method from "dgT*" to "Tsparse*"
1355 :    
1356 :    
1357 : bates 1595 2006-09-28 Douglas Bates <bates@R-project.org>
1358 :    
1359 :     * src/dppMatrix.h: Ensure definition of dspMatrix_validate is
1360 :     included.
1361 :    
1362 :     * src/init.c, inst/include/{Matrix.h,Matrix_stubs.h,cholmod.h}:
1363 :     Export C-callable functions used in Zt_create in lme4.
1364 :    
1365 : maechler 1592 2006-09-28 Martin Maechler <maechler@stat.math.ethz.ch>
1366 :    
1367 :     * DESCRIPTION (Version): 0.9975-1
1368 :    
1369 :     * tests/simple.R: less checks fail; using NA, found that our
1370 :     kronecker() is not base-compatible with NA's.
1371 :    
1372 :     * R/dMatrix.R: "Compare" method now implemented for all cases
1373 :    
1374 :     * R/Auxiliaries.R (indTri): == which([lower/upper].tri( * )) new utility
1375 :    
1376 :     * man/dtpMatrix-class.Rd: mention length of 'x' slot
1377 :    
1378 :     * src/dtpMatrix.c (dtpMatrix_validate): fix check
1379 :     * src/dspMatrix.c (dspMatrix_validate): ditto
1380 :    
1381 :     * R/dtTMatrix.R (gt2tT): fix ("l" -> "n")
1382 :     including coercion to [nl]tTMatrix.
1383 :    
1384 :     * R/diagMatrix.R (show): print a header line as for other classes.
1385 :    
1386 :     2006-09-27 Martin Maechler <maechler@stat.math.ethz.ch>
1387 :    
1388 :     * src/Makefile.win (SUBDIRS): fix typo
1389 :    
1390 : maechler 1583 2006-09-19 Martin Maechler <maechler@stat.math.ethz.ch>
1391 :    
1392 :     * DESCRIPTION (Date): ready to release 0.9975-0 to CRAN
1393 :    
1394 : bates 1577 2006-09-18 Douglas Bates <bates@stat.wisc.edu>
1395 :    
1396 :     * R/[CT]sparse.R (crossprod and tcrossprod): Handle the cases for x
1397 :     symmetric and y missing in R code using %*% (cholmod_aat doesn't
1398 :     accept a symmetric matrix).
1399 :     * tests/group-methods.R: Uncomment test of crossprod applied to
1400 :     lsCMatrix objects.
1401 :    
1402 : maechler 1575 2006-09-18 Martin Maechler <maechler@stat.math.ethz.ch>
1403 :    
1404 :     * R/AllClass.R (symmetricMatrix): add validity method (available
1405 :     in C for a long time). Many "n..Matrix": drop (wrong) validity arg.
1406 :    
1407 :     * src/lgCMatrix.c (lgCMatrix_validate): check 'x' slot (!)
1408 :    
1409 :     * tests/indexing.Rout.save:
1410 :     * tests/indexing.R: additions, mainly for 'lsparse'
1411 :    
1412 :     * R/diagMatrix.R (Diagonal) & coercion to lgTMatrix: fixes for NA
1413 :     case.
1414 :    
1415 :     * R/Auxiliaries.R (nz.NA): new utility now used in nnzero()
1416 :    
1417 : maechler 1571 2006-09-16 Martin Maechler <maechler@stat.math.ethz.ch>
1418 :    
1419 : maechler 1572 * R/sparseMatrix.R (prSpMatrix): print logical NAs "visibly"
1420 :     as 'N' (1-letter - Ok?)
1421 :    
1422 : maechler 1571 * tests/group-methods.R: add test for logical + NAs
1423 :    
1424 :     * R/dMatrix.R ("Compare"): fix to work with NA's
1425 :    
1426 :     * R/AllClass.R: "Cholesky" etc now inherit from MatrixFactorization.
1427 :    
1428 :     * src/lgCMatrix.c (ncsc_to_matrix): renamed from lcsc_to_matrix()
1429 :     which is implemented.
1430 :    
1431 : maechler 1565 2006-09-15 Martin Maechler <maechler@stat.math.ethz.ch>
1432 :    
1433 : maechler 1571 * src/chm_common.c: coerce logical <-> double instead of
1434 :     typecasting; needed for "l" matrix handling in cholmod.
1435 : maechler 1565
1436 : maechler 1571 * tests/other-pkgs.R (graph): small extension in "graph" checks.
1437 :    
1438 : maechler 1565 * R/sparseMatrix.R (graphNEL -> Tsparse): method for weight case.
1439 :     (Tsp2grNEL): other fixes needed
1440 :    
1441 : maechler 1548 2006-09-11 Martin Maechler <maechler@stat.math.ethz.ch>
1442 :    
1443 :     * R/AllClass.R ("nMatrix"): and subclasses for "nonzero pattern"
1444 :     Matrices, since "lMatrix", also "lsparseM" can have NA
1445 :     * R/ndenseMatrix.R, etc: new source files
1446 :     * man/nsparseMatrix-classes.Rd, etc: new help files
1447 :     * tests/: adaptions
1448 :     * src/chm_common.c (chm_dense_to_SEXP): and others:
1449 :     new 'Rkind' argument: "l*" and "d*" both use CHOLMOD_REAL
1450 : maechler 1582 * src/Csparse.c, etc: ditto
1451 : maechler 1548
1452 : bates 1546 2006-09-11 Douglas Bates <bates@R-project.org>
1453 :    
1454 :     * src/Mutils.[ch],init.c inst/include/*.h: Move the
1455 :     alloc_d**Matrix functions to the lme4 package.
1456 :    
1457 : bates 1543 2006-09-09 Douglas Bates <bates@R-project.org>
1458 :    
1459 :     * src/dsCMatrix.c (dsCMatrix_Cholesky): igoring LDL = FALSE now
1460 : maechler 1544 fixed
1461 : bates 1543
1462 : maechler 1544 2006-09-09 Martin Maechler <maechler@stat.math.ethz.ch>
1463 :    
1464 : maechler 1548 * R/lMatrix.R: new
1465 :    
1466 : maechler 1544 * R/sparseMatrix.R (Tsp2grNEL): do not yet use graph::foo()
1467 :    
1468 :     * R/dgeMatrix.R: do not define tcrossprod() methods for "matrix"
1469 : maechler 1582 * man/tcrossprod.Rd: ditto
1470 : maechler 1544
1471 : bates 1538 2006-09-08 Douglas Bates <bates@stat.wisc.edu>
1472 :    
1473 :     * inst/include/Matrix_stubs.c,Matrix.h: Add declarations and stubs
1474 :     for exported functions
1475 :     * src/Makefile, src/CHOLMOD/Lib/Makefile, src/Metis,CAMD,CCOLAMD:
1476 :     Remove partitioning algorithms for sparse matrix reordering. The
1477 :     copyright on the Metis code was problematic and the methods were
1478 :     rarely used.
1479 :     * src/triplet_to_col.[ch],MMHB.[ch]: Remove triplet_to_col. Such
1480 :     operations are now done entirely in CHOLMOD code.
1481 :    
1482 : bates 1517 2006-09-06 Douglas Bates <bates@R-project.org>
1483 :    
1484 :     * src/Mutils.h: Remove functions that are no longer used.
1485 :    
1486 : bates 1507 2006-09-04 Douglas Bates <bates@R-project.org>
1487 :    
1488 :     * src/dtCMatrix.c (dtCMatrix_validate): rename functions.
1489 :     * src/DEPS.mkf: update
1490 :    
1491 : maechler 1481 2006-09-02 Martin Maechler <maechler@stat.math.ethz.ch>
1492 :    
1493 :     * created branches/Matrix-for-R-2.3.x; on trunk: do
1494 :     * DESCRIPTION (Version): 0.9975-0
1495 :     (Depends): R (>= 2.4.0)
1496 :    
1497 : bates 1475 2006-09-01 Douglas Bates <bates@R-project.org>
1498 :    
1499 :     * R/sparseMatrix.R: Added direct method to CsparseMatrix from graphNEL
1500 :    
1501 : maechler 1472 2006-09-01 Martin Maechler <maechler@stat.math.ethz.ch>
1502 :    
1503 :     * R/sparseMatrix.R: add coercion from "ANY" to "sparseMatrix"
1504 :     * R/denseMatrix.R: add coercion from "ANY" to "denseMatrix"
1505 :    
1506 :     * R/Matrix.R ([): use nargs() to disambiguate M[i] and M[i,]
1507 :    
1508 :     2006-08-31 Martin Maechler <maechler@stat.math.ethz.ch>
1509 :    
1510 :     * R/sparseMatrix.R (Arith): moved Arith group method one-level up
1511 :     from "dsparse" to "sparse" and now go via "Csparse" instead of "dgC"
1512 : maechler 1582 * R/dsparseMatrix.R: ditto
1513 :     * R/Csparse.R: ditto
1514 : maechler 1472
1515 :     2006-08-31 Martin Maechler <maechler@stat.math.ethz.ch>
1516 :    
1517 :     * R/dMatrix.R (Compare): improve availability of "<", etc
1518 :     * R/Auxiliaries.R (asTuniq): new; also make use of R 2.4.x print(*,max)
1519 :    
1520 : maechler 1467 2006-08-30 Martin Maechler <maechler@stat.math.ethz.ch>
1521 :    
1522 :     * R/dgCMatrix.R: aargh: "Arith(<dgC>, numeric)" was wrong because
1523 :     of a 0-index which was used as 1-index (..hmm)
1524 :    
1525 :     * R/sparseMatrix.R (prSpMatrix): fix printing an all-0 sparse Matrix
1526 :    
1527 :     * R/Auxiliaries.R (all0, is0): for 0-testing in presence of NA's
1528 :     * R/Auxiliaries.R (isTriMat): use all0() for 0-testing.
1529 : maechler 1582 (.is.diagonal): ditto
1530 : maechler 1467
1531 :     * R/lgTMatrix.R: as("matrix", "lgTMatrix"): warn about NA's
1532 :    
1533 :     * R/Matrix.R (Matrix): also work for NA data
1534 :    
1535 : maechler 1455 2006-08-28 Martin Maechler <maechler@stat.math.ethz.ch>
1536 :    
1537 :     * R/Matrix.R (Matrix): + 'forceCheck' argument; dimnames setting
1538 :     in all cases.
1539 :    
1540 : bates 1453 2006-08-27 Douglas Bates <bates@R-project.org>
1541 :    
1542 :     * src/dense.[ch],init.c, R/ddenseMatrix.R, man/band.Rd
1543 :     (ddense_band): Added triu, tril and band for ddenseMatrix objects.
1544 :    
1545 : maechler 1447 2006-08-25 Martin Maechler <maechler@stat.math.ethz.ch>
1546 :    
1547 :     * src/Mutils.c (dup_mMatrix_as_dgeMatrix): added all subclasses of
1548 :     subclasses of "ddenseMatrix"
1549 :     * src/init.c et al: outcomment dtrM*_as_dge* and dsyM*_as_dge*_
1550 :     * R/ddenseMatrix.R et al: setAs("ddenseMatrix", "dgeMatrix", ..)
1551 :     instead of half dozen specialized ones.
1552 :    
1553 : bates 1445 2006-08-25 Douglas Bates <bates@R-project.org>
1554 :    
1555 :     * R/lmer.R (qqmath method): Bug fix provided by Emmanuel Tillard
1556 :     <tillard@cirad.fr> - ordering standard errors to match effects.
1557 :    
1558 : bates 1439 2006-08-24 Douglas Bates <bates@R-project.org>
1559 : bates 1431
1560 : bates 1439 * src/lsCMatrix.c (lsCMatrix_trans): Remove lsCMatrix_chol based
1561 :     on R_ldl.
1562 :     * R/lCholCMatrix.R,
1563 :     src/[dl]CholCMatrix.[ch],R_ldl.[ch],Metis_utils.[ch]: removed
1564 :     * src/dsCMatrix.c (dsCMatrix_to_dgTMatrix): use CHOLMOD
1565 :     * many files in ./R and ./src: Use more general version of
1566 :     dup_mMatrix_as_dgeMatrix to simplify method definitions.
1567 : bates 1442 * src/Mutils.c (dup_mMatrix_as_dgeMatrix): Add ddiMatrix,
1568 :     dtpMatrix, dspMatrix and dppMatrix conversions.
1569 :    
1570 : maechler 1447
1571 : bates 1439 2006-08-23 Douglas Bates <bates@R-project.org>
1572 :    
1573 :     * R/AllClass.R,lCholCMatrix.R,src/SOURCES_C.mkf,init.c,NAMESPACE:
1574 :     Remove classes lCholCMatrix and dCholCMatrix based on R_ldl code.
1575 : bates 1431 * src/dgeMatrix.c: Ensure 'factors' slot exists in result of
1576 :     dgeMatrix_crossprod (may need to do this in other places).
1577 :     * R/AllGeneric.R,dsCMatrix.R, src/dscMatrix.[ch]: Add Cholesky
1578 :     generic and method for dsCMatrix. Use CHOLMOD for chol().
1579 :    
1580 : bates 1414 2006-08-22 Douglas Bates <bates@R-project.org>
1581 :    
1582 :     * src/Mutils.c (dup_mMatrix_as_dgeMatrix): updated for general
1583 :     types of classed Matrices, matrices or numeric or logical vectors.
1584 : bates 1423 * src/init.c: register dup_mMatrix_as_dgeMatrix for coercions.
1585 :     * src/chm_common.c,Mutils.h (as_cholmod_factor): Move check_class
1586 :     to Mutils.h (as an inline) and change name to Matrix_check_class;
1587 :     fixes in as_cholmod_factor and chm_factor_to_SEXP.
1588 :     * src/dsCMatrix.[ch]: Use CHOLMOD for dsCMatrix_chol and
1589 :     dsCMatrix_matrix_solve. Comment out vestigial functions.
1590 :     * src/Csparse.c: use diag_P and uplo_P macros.
1591 : maechler 1447
1592 : bates 1405 2006-08-21 Douglas Bates <bates@R-project.org>
1593 :    
1594 :     * src/lmer.c (internal_mer_RZXinv): Fix memory leak caught by
1595 : maechler 1447 valgrind.
1596 : bates 1411 * tests/matprod.R: Add tests to verify that 'solve' and '%*%' are
1597 :     inverses.
1598 :     * src/sparseQR.c (sparseQR_validate): add new validation test, fix
1599 :     -Wall warnings.
1600 :     * src/dppMatrix.c,dtrMatrix.c,dgCMatrix.c,dgeMatrix.c,dspMatrix.c:
1601 :     Use dup_mMatrix_as_dgeMatrix.
1602 : maechler 1447
1603 : bates 1403 2006-08-20 Douglas Bates <bates@R-project.org>
1604 :    
1605 :     * src/sparseQR.c: Fix thinko in sparseQR_resid_fitted.
1606 :     * tests/sparseQR.R: Added
1607 :     * man/sparseQR-class.Rd: Document methods for qr.* generics
1608 :     * R/sparseQR.R: Return correct # of coefs; fix cut-and-paste errors
1609 :    
1610 : bates 1398 2006-08-19 Douglas Bates <bates@R-project.org>
1611 :    
1612 :     * NAMESPACE, R/sparseQR.R, src/init.c,sparseQR.[ch],SOURCES_C.mkf:
1613 :     Added methods for sparseQR for qr.qy, qr.qty, qr.coef, qr.resid
1614 :     and qr.fitted.
1615 :     * src/Mutils.[ch]: Added dup_mMatrix_as_dgeMatrix utility
1616 :     * src/dgCMatrix.c: Check for ordering before storing q in dgCMatrix_QR
1617 :    
1618 : maechler 1389 2006-08-18 Martin Maechler <maechler@stat.math.ethz.ch>
1619 :    
1620 :     * R/AllGeneric.R: add "qr" and "chol" generics; via 'trick' since
1621 :     the base version has no "..." argument.
1622 :    
1623 :     * R/sparseMatrix.R (prSpMatrix): fix the triangular unit diagonal case.
1624 :    
1625 :     * R/Matrix.R: define and
1626 :     * NAMESPACE: export as.numeric() and as.logical() methods.
1627 :     Let's hope these do not badly slow down something...
1628 :     Finally export the zapsmall() method.
1629 :    
1630 : bates 1388 2006-08-17 Douglas Bates <bates@R-project.org>
1631 :    
1632 :     * src/dgCMatrix.[ch] (dgCMatrix_matrix_solve), src/init.c,
1633 :     R/dgCMatrix.R: solve methods for dgCMatrix and dense RHS.
1634 :     * src/dtCMatrix.c :Remove code that is no longer used
1635 :     * R/dtCMatrix.R: Use C code for diagU2N in CsparseMatrix classes
1636 :    
1637 : bates 1370 2006-08-14 Douglas Bates <bates@R-project.org>
1638 :    
1639 : bates 1373 * src/Csparse.[ch],init.c (Csparse_to_logical): Added utilities
1640 :     Csparse_to_logical and Csparse_symmetric_to_general.
1641 :     * R/dgCMatrix.R,dsCMatrix.R,Csparse.R : Consolidate general
1642 : maechler 1389 coercion methods between CsparseMatrix and TsparseMatrix.
1643 : bates 1373
1644 :     2006-08-14 Douglas Bates <bates@R-project.org>
1645 :    
1646 : bates 1370 * R/dtCMatrix.R,dgCMatrix.R,Csparse.R src/init.c,dgCMatrix.[ch],
1647 :     Csparse.[ch],chm_common.c,dense.c : Use CHOLMOD code and methods
1648 :     for CsparseMatrix, TsparseMatrix, denseMatrix or matrix when
1649 :     possible.
1650 :    
1651 : bates 1368 2006-08-12 Douglas Bates <bates@R-project.org>
1652 :    
1653 :     * src/chm_common.[ch],Csparse.[ch],Tsparse.[ch],CHMfactor.c,dtTMatrix.c,
1654 :     dgTMatrix.c,dgCMatrix.c,dsCMatrix.c,dtTMatrix.c, R/dsTMatrix.R,
1655 :     Tsparse.R,Csparse.R,dgTMatrix.R,dsCMatrix.R,lsCMatrix.R:
1656 :     generalize conversions between TsparseMatrix, CsparseMatrix,
1657 :     denseMatrix and matrix. Preserve triangularity property and
1658 :     propagate Dimnames in the easy cases.
1659 :    
1660 : bates 1365 2006-08-10 Douglas Bates <bates@R-project.org>
1661 :    
1662 :     * src/lmer.c: adjust checks in glmer_init for S4SXP
1663 :     * tests/validObj.R: check of all(eq) should be all(eq@x) - worked
1664 :     before S4SXP but for the wrong reasons.
1665 :    
1666 : bates 1354 2006-08-08 Douglas Bates <bates@R-project.org>
1667 :    
1668 : bates 1360 * src/Csparse.c (Csparse_crossprod): tcrossprod result has stype = -1.
1669 :     Later modified to return the upper triangle only.
1670 :     * R/dgTMatrix.R: Remove vestigial crossprod and tcrossprod methods.
1671 : maechler 1389
1672 : bates 1352 2006-08-07 Douglas Bates <bates@R-project.org>
1673 :    
1674 :     * src/Csparse.c (Csparse_crossprod): Set stype on result to avoid
1675 :     R-level conversion to a sparse symmetric class.
1676 :     * R/Tsparse.R,R/Csparse.R (crossprod and tcrossprod methods):
1677 :     Remove conversion to sparse symmetric classes (now done in C code).
1678 :    
1679 : maechler 1349 2006-08-07 Martin Maechler <maechler@stat.math.ethz.ch>
1680 :    
1681 : maechler 1351 * R/dgCMatrix.R: disable old crossprod and tcrossprod methods
1682 :     * man/band.Rd: adapt the \dontshow{} unit test.
1683 :    
1684 :     2006-08-07 Martin Maechler <maechler@stat.math.ethz.ch>
1685 :    
1686 : maechler 1349 * DESCRIPTION (Version): 0.995-14 for CRAN
1687 :    
1688 :     * tests/other-pkgs.R: oops: library(Matrix) outside *if* !
1689 :    
1690 :     * R/sparseMatrix.R (Tsp2grNEL): fixed Tsparse -> graph coercion
1691 :     * tests/other-pkgs.R: more checks, sparseMatrix -> graph
1692 :    
1693 :     * R/Auxiliaries.R (as_Tsparse, as_Rsparse): new
1694 :     * R/Tsparse.R (tril, triu, band): methods
1695 : bates 1352 * R/dgRMatrix.R (tril, ...): ditto
1696 :     * man/band.Rd: ditto
1697 : maechler 1349
1698 :     2006-08-04 Martin Maechler <maechler@stat.math.ethz.ch>
1699 :    
1700 :     * R/Matrix.R (head, tail): directly use utils:::head.matrix
1701 :     to be up-to-date automatically.
1702 :    
1703 : maechler 1346 2006-08-03 Martin Maechler <maechler@stat.math.ethz.ch>
1704 :    
1705 :     * DESCRIPTION (Version): 0.995-13 to be released to CRAN
1706 :    
1707 :     * DESCRIPTION (Lazydata): no, instead of 'yes' because it fails for:
1708 :     * data/CAex.R, inst/external/CAex_slots.rda: replacing data/CAex.rda
1709 :     * data/KNex.R, inst/external/KNex_slots.rda: replacing data/KNex.rda
1710 :     such that the S4 objects are always created by the current version
1711 :     of R and 'Matrix' class definitions.
1712 :    
1713 : bates 1342 2006-08-01 Douglas Bates <bates@R-project.org>
1714 :    
1715 :     * R/lmer.R (LMEoptimize method), tests/lmer.R,
1716 : maechler 1346 inst/external/test3comp.rda: Added warnings for convergence on
1717 : bates 1342 boundary and test cases.
1718 :    
1719 :     * src/lmer.c (mer_postVar): Modified to return the variances that
1720 :     are marginal to the fixed effects, not conditional on them (which
1721 :     is what the bVar slot contents represent).
1722 :    
1723 : bates 1338 2006-07-31 Douglas Bates <bates@R-project.org>
1724 :    
1725 :     * NAMESPACE, src/lmer.c, R/lmer.R (hatTrace): Add the hatTrace
1726 :     function which calls the C function mer_hat_trace2.
1727 : maechler 1346
1728 : bates 1342 * man/ranef.Rd: Include description of "postVar" argument and
1729 :     producing a caterpillar plot.
1730 : bates 1338
1731 : maechler 1335 2006-07-31 Martin Maechler <maechler@stat.math.ethz.ch>
1732 :    
1733 :     * NAMESPACE: change "correlation" to "corMatrix"
1734 :     * R/AllClass.R: to avoid clash with S3 class in 'nlme'.
1735 : bates 1352 * R/dpoMatrix.R: ditto
1736 :     * R/lmer.R: ditto
1737 : maechler 1335
1738 : bates 1338 2006-07-28 Douglas Bates <bates@R-project.org>
1739 :    
1740 :     * src/lmer.c (internal_mer_RZXinv): Split the calculation of the
1741 :     RZXinv slot's contents into a separate internal function that can
1742 :     be used in mer_hat_trace.
1743 :    
1744 : maechler 1331 2006-07-22 Martin Maechler <maechler@stat.math.ethz.ch>
1745 :    
1746 :     * R/Matrix.R: Coercions "Matrix" -> (sparse|dense)Matrix
1747 :     via new smart
1748 :     * R/Auxiliaries.R (as_Csparse, as_dense, .M.shapse): new
1749 :     utility functions.
1750 :    
1751 :    
1752 : maechler 1330 2006-07-21 Martin Maechler <maechler@stat.math.ethz.ch>
1753 :    
1754 : maechler 1331 * R/Csparse.R (tril, triu, band): do return *triangular* classed
1755 :     matrices when appropriate; band() even symmetric ones.
1756 :     (replCmat): extend to potentially all "CsparseMatrix"
1757 :     * R/Tsparse.R (replTmat): extend to all "TsparseMatrix"; hence
1758 :     allow subassignment for special sparse matrices.
1759 :    
1760 :     * R/Auxiliaries.R (as_geClass): factor out the .M.kind() functionality
1761 :    
1762 : maechler 1330 * src/lmer.c (mer_MCMCsamp, glmer_MCMCsamp): new 'verbose'
1763 :     argument; in glmer_*(): print only if(verbose).
1764 :    
1765 :     speed-optimize a few places by moving REAL(.) out of loops.
1766 :    
1767 :     * src/lmer.h, src/init.h, R/lmer.R: related to above.
1768 :    
1769 : maechler 1329 2006-07-20 Martin Maechler <maechler@stat.math.ethz.ch>
1770 :    
1771 :     * R/Matrix.R("["): disable ("Matrix", i = "logical", j = "missing"),
1772 :     since that wrongly triggers also for M[ logi , ]
1773 :    
1774 :     * R/denseMatrix.R: "[" methods now also work e.g. when indexing
1775 :     a symmetric matrix that results in a non-symmetric one.
1776 :     * R/Auxiliaries.R (as_geClass): new function used in "[" above.
1777 :    
1778 :     * R/dMatrix.R: make round(M) work as round(M, 0)
1779 :    
1780 :     * R/dgTMatrix.R (image): coordinate system and axis now use
1781 :     1-based indices, not 0-based ones.
1782 :    
1783 :     * R/Tsparse.R (.ind.prep for "["): get rid of max(<empty>) warning.
1784 :     * tests/indexing.R: test it.
1785 :    
1786 :     * NAMESPACE: export isSymmetric(); has been a generic in "base" for a while;
1787 :     * man/isSymmetric-methods.Rd: and document it.
1788 :    
1789 :     * R/SparseM-conv.R: added coercion methods for some 'SparseM' matrices.
1790 :     * man/SparseM-conv.Rd: docu them
1791 :    
1792 :     * tests/other-pkgs.R: renamed from tests/graph.R and add example
1793 :     for 'SparseM' conversions
1794 :    
1795 :     2006-07-17 Douglas Bates <Douglas.Bates@R-project.org>
1796 :    
1797 :     * R/Matrix.R (head): added head() and tail() methods.
1798 :    
1799 :     2006-07-17 Martin Maechler <maechler@stat.math.ethz.ch>
1800 :    
1801 :     * DESCRIPTION (Version): 0.995-12 released to CRAN
1802 :    
1803 : maechler 1319 2006-07-15 Martin Maechler <maechler@stat.math.ethz.ch>
1804 :    
1805 :     * tests/simple.R: add check for correct dsT -> dgT coercion;
1806 :     add check for correct printing of symmetric sparse matrices.
1807 :    
1808 :     * R/Auxiliaries.R (non0ind): return *all* non-0 entry indices also
1809 :     for sparse symmetric matrices.
1810 :    
1811 :     * src/dsTMatrix.c (dsTMatrix_as_dgTMatrix): do not copy the
1812 :     diagonal twice.
1813 :    
1814 : bates 1316 2006-07-11 Douglas Bates <Douglas.Bates@R-project.org>
1815 :    
1816 :     * src/dsTMatrix.c (dsTMatrix_as_dgTMatrix): Fix a case of INTEGER
1817 : maechler 1319 being applied to the x slot (detected by Brian Ripley).
1818 : bates 1316
1819 : maechler 1315 2006-07-10 Martin Maechler <maechler@stat.math.ethz.ch>
1820 :    
1821 :     * src/dgCMatrix.c (dgCMatrix_validate): 'p' slot must have correct length.
1822 :    
1823 :     * R/Auxiliaries.R (isTriC): fix buglet (we were 1-based!)
1824 :    
1825 :     2006-07-08 Martin Maechler <maechler@stat.math.ethz.ch>
1826 :    
1827 :     * src/lgCMatrix.c (lgCMatrix_diag): new function
1828 :     * R/lgCMatrix.R (diag): for new method
1829 :    
1830 :     * R/AllClass.R (TsparseMatrix): do use Tsparse_validate
1831 :     ==> construction of illegal "*gTMatrix" via new() should
1832 :     now be much less easy:
1833 :     * tests/Class+Meth.R: assertError() for some illegal "dgT*"
1834 :    
1835 :     * R/Matrix.R (Matrix): Matrix(0, nrow,ncol) now "goes sparse"
1836 :     directly.
1837 :     * man/Matrix.Rd: documents it.
1838 :    
1839 : bates 1311 2006-07-06 Douglas Bates <bates@R-project.org>
1840 :    
1841 :     * src/pedigree.c (pedigree_inbreeding): Correction in
1842 :     initialization. This function is not currently being used and is
1843 :     not fully tested.
1844 :    
1845 : bates 1312 * NAMESPACE, R/{AllClass.R,lmer.R}, src/{init.c,lmer.c}:
1846 :     Introduced the glmer class. Added code for mcmcmsamp on glmer
1847 :     objects. Modified validity check on pedigree objects to account
1848 :     for nonparallel patterns of missingness of parents.
1849 : bates 1311
1850 : bates 1313 * man/{lmer-class.Rd,mcmcsamp.Rd}: Update documentation for glmer
1851 :     class.
1852 : maechler 1315
1853 :     2006-07-01 Martin Maechler <maechler@stat.math.ethz.ch>
1854 :    
1855 :     * R/pMatrix.R: coercion pMatrix -> Tsparse
1856 :    
1857 : bates 1300 2006-06-12 Douglas Bates <bates@R-project.org>
1858 :    
1859 : maechler 1319 * DESCRIPTION (Version): 0.995-11 released to CRAN
1860 :    
1861 : bates 1300 * R/lmer.R (mcmcsamp method): Corrected arrangments of names on
1862 :     the output from mcmcsamp.
1863 :    
1864 : bates 1298 2006-06-10 Douglas Bates <bates@R-project.org>
1865 :    
1866 : bates 1300 * R/lmer.R (simulestimate): added C code for calculating the trace
1867 :     of the hat matrix.
1868 : bates 1298
1869 : maechler 1295 2006-06-09 Martin Maechler <maechler@stat.math.ethz.ch>
1870 :    
1871 :     * R/diagMatrix.R (setAs): define coercion methods to sparse matrix
1872 :     classes.
1873 : maechler 1315 * R/sparseMatrix.R etc: multiplication of diagonal and sparse
1874 : maechler 1295
1875 : maechler 1290 2006-06-08 Martin Maechler <maechler@stat.math.ethz.ch>
1876 :    
1877 :     * R/dgTMatrix.R (colSums): etc. All four of
1878 :     colSums(), rowSums(), colMeans(), rowMeans() now should work for
1879 :     all "Matrices".
1880 :    
1881 : bates 1288 2006-06-01 Douglas Bates <bates@stat.wisc.edu>
1882 :    
1883 :     * R/lmer.R (panel.ci): Add a reference line at zero and a
1884 :     background grid to the qqmath plot of ranef.lmer.
1885 :    
1886 : bates 1287 2006-05-30 Douglas Bates <bates@stat.wisc.edu>
1887 : bates 1284
1888 : bates 1287 * R/lmer.R (expandSlash): Functions (non-exported) to allow nested
1889 :     grouping factors to be specified in the formula as (1|foo/bar).
1890 :    
1891 :     2006-05-27 Douglas Bates <bates@stat.wisc.edu>
1892 :    
1893 : bates 1284 * R/lmer.R (findbars and others): Change check of is.numeric to
1894 :     !is.language to resolve the bug reported by Jacob Wegelin.
1895 :    
1896 :     * src/pedigree.c (pedigree_inbreeding): Initial implementation of
1897 :     code to evaluate inbreeding coefficients without calculating T,
1898 :     based on code in Sargolzaei and Iwaisaki's paper.
1899 :    
1900 : bates 1283 2006-05-27 Douglas Bates <bates@stat.wisc.edu>
1901 :    
1902 :     * R/{lmer.R,AllGeneric.R}, src/{init.c,lmer.[ch]}: Added local
1903 :     generic and mer methods for isNested and denomDF. This denomDF was
1904 :     an attempt to emulate that in lme but I don't think that makes
1905 :     sense. Use the trace of the hat matrix instead.
1906 :    
1907 : maechler 1271 2006-05-17 Martin Maechler <maechler@stat.math.ethz.ch>
1908 :    
1909 :     * R/sparseMatrix.R: Matrix <-> graph methods: can no longer use
1910 :     the C code depending on a slot structure that's no longer valid.
1911 : bates 1352 * src/dgTMatrix.c: ditto (also: src/init.c src/dgTMatrix.h)
1912 : maechler 1271
1913 :    
1914 : bates 1268 2006-05-17 Douglas Bates <bates@stat.wisc.edu>
1915 :    
1916 :     * R/{AllGeneric.R,Csparse.R},man/band.Rd,NAMESPACE: changed name
1917 :     of lowerTriMatrix generic and methods to tril (also upper to triu)
1918 :     and added a general band extractor.
1919 :    
1920 : bates 1267 2006-05-16 Douglas Bates <bates@stat.wisc.edu>
1921 :    
1922 :     * R/pedigree.R (pedigree): Replace sire and dam values outside the
1923 :     allowable range with NAs. Added a corresponding check in the
1924 :     validity check for the pedigree class.
1925 :    
1926 :     * R/[CT]sparse.R ([t]crossprod): The result of single-argument
1927 :     crossprod methods now inherits from symmetricMatrix.
1928 :    
1929 : bates 1265 2006-05-15 Douglas Bates <bates@stat.wisc.edu>
1930 :    
1931 :     * R/AllGeneric.R (lowerTriMatrix): Added (but did not export)
1932 :     generics lowerTriMatrix and upperTriMatrix along with methods for
1933 :     the Csparse virtual class. Also added a C function Csparse_band
1934 :     that implements these methods by calling cholmod_band.
1935 :    
1936 : maechler 1264 2006-05-15 Martin Maechler <maechler@stat.math.ethz.ch>
1937 :    
1938 :     * R/Tsparse.R ("["): column or row subsetting; @Dimnames[k] got
1939 :     erased when it was NULL. This led to invalid subselections!
1940 :    
1941 : bates 1259 2006-04-25 Douglas Bates <bates@stat.wisc.edu>
1942 :    
1943 :     * R/dtCMatrix.R: avoid coercion of dtCMatrix object to dgCMatrix
1944 :     in method for "t" so as not to lose the unit diagonal property.
1945 :    
1946 : bates 1257 2006-04-19 Douglas Bates <bates@stat.wisc.edu>
1947 :    
1948 :     * R/lmer.R, R/AllGeneric.R, NAMESPACE: Remove the postVar generic
1949 :     and methods. This is now an option to the ranef method for the
1950 :     mer class.
1951 :    
1952 :     * src/cs_utils.c: Ensure that the nz component is -1 for a
1953 :     compressed column-oriented matrix. Minor formatting cleanup.
1954 :    
1955 :     * man/lmer-class.Rd: Document the qqmath method for ranef.lmer
1956 :     objects.
1957 :    
1958 : maechler 1253 2006-04-19 Martin Maechler <maechler@stat.math.ethz.ch>
1959 :    
1960 :     * R/Auxiliaries.R (diagU2N): new for the solve() methods in
1961 :     * R/dtCMatrix.R: where dgC -> dgT coercion now preserves diag = "U".
1962 :    
1963 : bates 1251 2006-04-15 Douglas Bates <bates@stat.wisc.edu>
1964 :    
1965 :     * src/cs.[ch],src/cs_utils.[ch] : Added Tim Davis' CSparse library
1966 :     in cs.[ch] and utilities to interface to that code in cs_utils.[ch].
1967 :    
1968 :     * R/dtCMatrix.R, src/dtCMatrix.[ch] : CSparse-based solve methods
1969 :     for the dtCMatrix class.
1970 : maechler 1253
1971 : bates 1247 2006-04-12 Douglas Bates <bates@stat.wisc.edu>
1972 :    
1973 :     * R/pedigree.R, R/AllClass.R, NAMESPACE: added a pedigree class
1974 :     and methods for it.
1975 :    
1976 : maechler 1245 2006-04-12 Martin Maechler <maechler@stat.math.ethz.ch>
1977 :    
1978 :     * R/dgCMatrix.R: add storage.mode(.) <- "double" for "matrix"
1979 :     arguments, such that M %*% 1:6 now works
1980 :     * Tests/matprod.R: test the above
1981 :    
1982 : bates 1244 2006-04-03 Douglas Bates <bates@stat.wisc.edu>
1983 : bates 1243
1984 :     * R/lmer.R (qqmath,ranef.lmer-method): added a qqmath method for
1985 :     the ranef.lmer class.
1986 :    
1987 :     * R/AllClass.R, NAMESPACE, R/lmer.R: Added a postVar generic and
1988 :     methods to extract the posterior variances from the bVar slot.
1989 :    
1990 : maechler 1238 2006-03-30 Martin Maechler <maechler@stat.math.ethz.ch>
1991 :    
1992 :     * R/dtCMatrix.R: allow coercion from dgC* to triangular (dtC*)
1993 :     * R/dsCMatrix.R: and symmetric (dsC*) 'Csparse' matrices.
1994 :    
1995 :     * R/Tsparse.R: Tsparse* -> Csparse* coercion now works and is tested in
1996 :     * tests/simple: (extended)
1997 :    
1998 :     * R/sparseMatrix.R (isTriangular): now using much improved
1999 :     * R/Auxiliaries.R (isTriC): new triangularity check for *CMatrix
2000 :    
2001 : bates 1236 2006-03-23 Douglas Bates <bates@stat.wisc.edu>
2002 :    
2003 :     * src/dsyMatrix.c (dsyMatrix_as_dspMatrix): Propagate DimNames
2004 :     (problem report from Franklin Parlamis). This should be done
2005 : maechler 1238 generally.
2006 : bates 1236
2007 : bates 1234 2006-03-21 Douglas Bates <bates@stat.wisc.edu>
2008 :    
2009 :     * R/AllClass.R,lmer.R: Change the name of the lmer.ranef class to
2010 :     ranef.lmer (like summary.lmer). Add the coef.lmer class and
2011 :     update the plot methods.
2012 :    
2013 : bates 1232 2006-03-20 Douglas Bates <bates@stat.wisc.edu>
2014 :    
2015 :     * R/lmer.R (resid and ranef methods): Added methods for the
2016 :     "residuals" and "resid" generic but only for linear mixed model
2017 :     fits. Changed the ranef method to return a list of data frames so
2018 :     that the plot methods now work.
2019 :    
2020 : bates 1230 2006-03-16 Douglas Bates <bates@bates2>
2021 :    
2022 :     * src/dpoMatrix.c (dpoMatrix_chol): Require n > 0 in call to
2023 :     dpotrf - otherwise the BLAS on Mac OS X complains and quits.
2024 :    
2025 :     * DESCRIPTION (Date): New release
2026 :    
2027 : maechler 1228 2006-03-15 Martin Maechler <maechler@stat.math.ethz.ch>
2028 :    
2029 :     * DESCRIPTION (Version): 0.995-6 -- to be released to CRAN
2030 :    
2031 :     * data/KNex.rda: replacing 'mm' and 'y' by KNex <- list(mm=mm, y=y)
2032 :     * man/KNex.Rd: and other help files
2033 :     * tests/*.R: several ones needed adaption
2034 : bates 1352 * inst/doc/Comparisons.Rnw: ditto
2035 : maechler 1228
2036 : maechler 1226 2006-03-11 Martin Maechler <maechler@stat.math.ethz.ch>
2037 :    
2038 :     * R/dgCMatrix.R (replCmat): "[<-" methods for dgCMatrix
2039 :    
2040 :     * tests/indexing.R: tests for new [<- methods for sparse matrices.
2041 :    
2042 :     2006-03-10 Martin Maechler <maechler@stat.math.ethz.ch>
2043 :    
2044 :     * R/dgTMatrix.R (replTmat): "[<-" methods for dgTMatrix
2045 :    
2046 :     * R/Tsparse.R (.ind.prep): fix out-of-range indexing
2047 :    
2048 :     2006-03-08 Martin Maechler <maechler@stat.math.ethz.ch>
2049 :    
2050 :     * R/dMatrix.R: enable things like M [ M < 10 ]
2051 :     * R/dgeMatrix.R: implement it
2052 :    
2053 : maechler 1222 2006-03-06 Martin Maechler <maechler@stat.math.ethz.ch>
2054 :    
2055 :     * R/AllClass.R: define "summary.mer" and "*.lmer"
2056 :     * R/lmer.R (summary): summary(<mer>) computes & returns the above;
2057 :     * R/lmer.R (show): now works with summary()
2058 :    
2059 :     2006-03-04 Martin Maechler <maechler@stat.math.ethz.ch>
2060 :    
2061 :     * R/dgCMatrix.R: finally direct "Arith" dgC o dgC
2062 :     * R/Auxiliaries.R (WhichintersectInd): and other utilities to
2063 :     support the above
2064 :    
2065 : bates 1213 2006-02-07 Douglas Bates <bates@stat.wisc.edu>
2066 :    
2067 :     * R/lmer.R (lmer): fix initial values of offset and weights for glm.fit.
2068 :     Use glmFit$prior.weights for weights in a glmm.
2069 :     Allow an option usePQL = FALSE to skip the PQL steps for the
2070 :     Laplace method (and, in time, the AGQ method).
2071 :    
2072 :     * src/lmer.c (mer_factor): Move downdating and factoring of XtX
2073 :     into a separate function internal_mer_Xfactor to be able to call
2074 :     it from internal_bhat.
2075 :    
2076 : maechler 1200 2006-01-23 Martin Maechler <maechler@stat.math.ethz.ch>
2077 :    
2078 :     * tests/Class+Meth.R (tstMatrixClass): function for much better
2079 :     testing; now again of all actual classes.
2080 :    
2081 :     * src/Mutils.c (MAKE_TRIANGULAR_BODY, MAKE_SYMMETRIC_BODY):
2082 :     use macros and define make_d_matrix_* and make_i_matrix_*
2083 :     where _i_ is for the ldense routines:
2084 :    
2085 :     * src/ldense.c (ltrMatrix_as_lgeMatrix): provide functions
2086 :     * src/ldense.c (lsyMatrix_as_lgeMatrix):
2087 :    
2088 :     * R/ldenseMatrix.R: use the above in setAs(*,"lgeMatrix")
2089 :    
2090 :    
2091 : maechler 1174 2006-01-16 Martin Maechler <maechler@stat.math.ethz.ch>
2092 :    
2093 :     * R/Matrix.R (Matrix): has become much "smarter" now auto-producing
2094 :     many different kinds of matrices.
2095 :     * R/*.R: quite a few new methods were needed for R CMD check with
2096 :     new Matrix(). Very good for users playing around.
2097 :    
2098 :    
2099 : maechler 1165 2006-01-15 Martin Maechler <maechler@stat.math.ethz.ch>
2100 :    
2101 :     * src/dgeMatrix.c (dMatrix_validate): new
2102 :     * src/Mutils.c (dense_nonpacked_validate): new
2103 :    
2104 :     * src/dtrMatrix.c (dtrMatrix_validate): improved/fixed
2105 :    
2106 :    
2107 :     2006-01-14 Douglas Bates <bates@stat.wisc.edu>
2108 :    
2109 :     * R/AllClass.R (compMatrix), (generalMatrix): new virtual classes
2110 :    
2111 : bates 1123 2006-01-07 Douglas Bates <bates@stat.wisc.edu>
2112 : bates 1119
2113 : maechler 1127 * DESCRIPTION (Version): 0.99-6 released to CRAN
2114 :    
2115 : bates 1119 * src/dgBCMatrix.c (cscb_trcbsm): Fix due to Peter Dalgaard for
2116 :     segfault in cases with multiple non-nested grouping factors.
2117 :    
2118 : maechler 1109 2006-01-03 Martin Maechler <maechler@stat.math.ethz.ch>
2119 :    
2120 :     * DESCRIPTION (Version): 0.99-4 to be released to CRAN
2121 :     (Depends): also on 'utils'
2122 :    
2123 :     * R/AllClass.R (diagonalMatrix): new class with "ddi*" and "ldi*"
2124 :     * R/diagMatrix.R (Diagonal): constructor and methods for
2125 :     diagonal matrices
2126 :    
2127 :     * R/ltTMatrix.R: new "minimal methods"
2128 :    
2129 : maechler 1091 2005-12-12 Martin Maechler <maechler@stat.math.ethz.ch>
2130 :    
2131 :     * R/AllGeneric.R (tcrossprod): 2-argument version; here, and for
2132 :     all methods (and help files).
2133 :    
2134 : maechler 1084 2005-12-09 Martin Maechler <maechler@stat.math.ethz.ch>
2135 :    
2136 :     * R/Auxiliaries.R (dimNamesCheck): fixed thinko -> bug
2137 :     for case (dimn. op no_dimn.)
2138 :    
2139 :     2005-11-14 Douglas Bates <bates@stat.wisc.edu>
2140 :    
2141 : maechler 1174 * DESCRIPTION (Version): 0.99-2 released to CRAN
2142 : maechler 1084
2143 : bates 988 2005-10-21 Douglas Bates <bates@stat.wisc.edu>
2144 :    
2145 :     * R/lmer.R (simulate method): Fixed a drop=FALSE problem reported
2146 :     by Julian Faraway.
2147 :    
2148 : maechler 976 2005-10-06 Martin Maechler <maechler@stat.math.ethz.ch>
2149 :    
2150 :     * R/Auxiliaries.R (try_as): new utility
2151 :     * R/sparseMatrix.R: use try_as() in coercion to original class
2152 :    
2153 : maechler 956 2005-09-30 Martin Maechler <maechler@stat.math.ethz.ch>
2154 :    
2155 :     * src/dgCMatrix.c (double_to_csc): and dgeMatrix_to_csc()
2156 :    
2157 :     2005-09-29 Martin Maechler <maechler@stat.math.ethz.ch>
2158 :    
2159 :     * R/Auxiliaries.R (dimNamesCheck): added
2160 :    
2161 :     * R/Matrix.R (as.array), (as.vector): new
2162 :    
2163 : maechler 954 2005-09-28 Martin Maechler <maechler@stat.math.ethz.ch>
2164 :    
2165 :     * R/Matrix.R (Matrix): get logical argument 'sparse' with a smart
2166 : maechler 956 default.
2167 :     * R/AllClass.R: move 'factors' slot toplevel "Matrix";
2168 :     "pMatrix" now contains "sparseMatrix"
2169 : maechler 954
2170 : maechler 948 2005-09-26 Martin Maechler <maechler@stat.math.ethz.ch>
2171 :    
2172 :     * tests/Class+Meth.R: new tests; t(t(m)) == m
2173 :    
2174 :     * src/dtCMatrix.c (tsc_transpose): add forgotten "diag" slot
2175 :    
2176 :     * src/dsTMatrix.c (dsTMatrix_as_dsCMatrix): bad typo (segfault!)
2177 :     * src/dtTMatrix.c (dtTMatrix_as_dtCMatrix): new
2178 :    
2179 :     * R/dspMatrix.R: typo in "t" method
2180 :    
2181 : maechler 925 2005-09-18 Douglas Bates <bates@wisc.edu>
2182 :    
2183 :     * R/AllClass.R (TsparseMatrix), CsparseM* and RsparseM*
2184 :     * R/Tsparse.R: instead of R/gTMatrix.R
2185 :     * R/Csparse.R: new
2186 :     * src/Tsparse.c (Tsparse_to_Csparse): new; -> cholmod_()
2187 :     * src/Tsparse.c: new; many trivial methods calling cholmod_()
2188 :     * src/Csparse.c (Csparse_to_Tsparse), transpose, (mat|cross)prod:
2189 :     via cholmod
2190 :    
2191 :     2005-09-16 Martin Maechler <maechler@stat.math.ethz.ch>
2192 :    
2193 :     * R/Auxiliaries.R (non0ind): new function using new C code
2194 :     * src/dgCMatrix.c (compressed_non_0_ij): new utility
2195 :    
2196 : bates 917 2005-09-15 Douglas Bates <bates@localhost.localdomain>
2197 :    
2198 :     * src/chm_common.h: header file required by all C sources that
2199 : maechler 1174 call CHOLMOD functions. It defines a cholmod_common structure
2200 : bates 917 called 'c' whose address is passed as the last argument to
2201 :     (virtually) every CHOLMOD function.
2202 :    
2203 :     * src/Pattern.c: Simple example of the use of CHOLMOD.
2204 :    
2205 :     * src/init.c: initialize and finalize the cholmod_common structure.
2206 :    
2207 :     * src/Makefile: Added source packages CHOLMOD UMFPACK AMD COLAMD
2208 :     LDL and CCOLAMD from the U. of Florida sparse matrix library.
2209 :    
2210 : maechler 908 2005-09-08 Martin Maechler <maechler@stat.math.ethz.ch>
2211 :    
2212 :     * inst/test-tools.R: new file collecting the utility functions used
2213 :     in ./tests/*.R
2214 :    
2215 :     * R/ddenseMatrix.R (cbind2): new methods for "numeric" and "matrix"
2216 :     * R/Matrix.R (cbind2): methods for NULL and missing
2217 :    
2218 : maechler 886 2005-08-31 Martin Maechler <maechler@stat.math.ethz.ch>
2219 :    
2220 :     * R/AllClass.R: new "index" class for "[" and "[<-":
2221 :     First cut at "symmetricMatrix" and "triangularMatrix"
2222 :     * R/gTMatrix.R (.ind.prep): new function;
2223 : maechler 1174 Logical and character indexing now work too.
2224 : maechler 886 * R/Matrix.R: cheap "[<-" methods for denseMatrix now work
2225 :     * tests/indexing.R: new, including *.Rout.save
2226 :     * tests/dgTMatrix.R: new
2227 :    
2228 : bates 876 2005-08-29 Douglas Bates <bates@wisc.edu>
2229 :    
2230 :     * src/dgTMatrix.c (graphNEL_as_dgTMatrix): Corrected the position
2231 :     indicator pos not being updated. Also enforced upper triangular
2232 :     for symmetric case. Need to coerce edges component of elements of
2233 :     edge list - grr! (Why don't they define their classes cleanly?)
2234 :    
2235 : maechler 871 2005-08-26 Martin Maechler <maechler@stat.math.ethz.ch>
2236 :    
2237 :     * R/Matrix.R: added first "[<-" methods; not yet functional
2238 : bates 1352 * R/denseMatrix.R: ditto
2239 : maechler 871 * man/Subassign-methods.Rd: new help file for these
2240 :    
2241 :     2005-08-25 Martin Maechler <maechler@stat.math.ethz.ch>
2242 :    
2243 :     * DESCRIPTION (Version): 0.98-6
2244 :    
2245 :     * R/denseMatrix.R: new file for "[" fallback methods for all dense
2246 :     matrices.
2247 :    
2248 : maechler 868 2005-08-19 Martin Maechler <maechler@stat.math.ethz.ch>
2249 :    
2250 :     * src/lgCMatrix.c (lcsc_to_matrix): new; need for
2251 :     as( <logical>, "matrix")
2252 :    
2253 :     * R/pMatrix.R: coercion to "lgTMatrix"
2254 :    
2255 :     * R/gTMatrix.R: new virtual class to define "[" methods for.
2256 :     * man/gTMatrix-class.Rd:
2257 :     * General slight re-organization of where "[" methods are defined.
2258 :     more to come.
2259 :    
2260 : maechler 871 2005-08-18 Douglas Bates <bates@wisc.edu>
2261 : maechler 868
2262 : maechler 1174 * DESCRIPTION (Version): 0.98-5 released to CRAN
2263 : maechler 871
2264 :     * src/dgTMatrix.c (graphNEL_as_dgTMatrix): add first graphNEL methods
2265 :     * .....
2266 :    
2267 : bates 863 2005-08-18 Douglas Bates <bates@localhost.localdomain>
2268 :    
2269 :     * R/lmer.R: Corrected naming scheme in mcmcsamp to work with lmer
2270 :     or glmer objects.
2271 :    
2272 : maechler 860 2005-08-17 Martin Maechler <maechler@stat.math.ethz.ch>
2273 :    
2274 :     * DESCRIPTION (Version): 0.98-4 : upload to CRAN
2275 :    
2276 :     2005-08-16 Douglas Bates <bates@localhost.localdomain>
2277 :    
2278 :     * R/HBMM.R: finish re-writing R-only code.
2279 :    
2280 : bates 854 2005-08-15 Douglas Bates <bates@localhost.localdomain>
2281 :    
2282 :     * man/externalFormats.Rd: move documentation for writeHB and
2283 :     writeMM here.
2284 :    
2285 :     * src/mmio.c: replace inclusion of <malloc.h> by <stdlib.h>
2286 :     (suggested by Paul Roecker).
2287 :    
2288 :     * tests/validObj.R (assertError): Comment out test that is failing
2289 :     after recent changes in r-devel.
2290 :    
2291 : maechler 860
2292 : maechler 848 2005-08-11 Martin Maechler <maechler@stat.math.ethz.ch>
2293 :    
2294 :     * R/AllClass.R: intermediate virtual class "denseMatrix"
2295 :     * man/denseMatrix-class.Rd
2296 :     * NAMESPACE: export it, and also export
2297 :     * man/unused-classes.Rd: "iMatrix", "zMatrix" and "ldenseMatrix"
2298 :    
2299 : bates 846 2005-08-10 Douglas Bates <bates@wisc.edu>
2300 :    
2301 : maechler 848 * DESCRIPTION (Version): 0.98-3 to CRAN
2302 :    
2303 : bates 846 * src/dtrMatrix.c (dtrMatrix_validate): fixed up validation and
2304 :     matrix_solve code (which was really, really wrong).
2305 :    
2306 : bates 835 2005-08-07 Douglas Bates <bates@wisc.edu>
2307 : maechler 834
2308 :     * DESCRIPTION (Version): 0.98-2
2309 :    
2310 :     * R/HBMM.R (readHB), (readMM): read Matrix Market formats
2311 :    
2312 :     * R/lmer.R (abbrvNms): new
2313 :     * R/lmer.R (mcmcsamp): allow transformed parameters
2314 : bates 835 * src/HBMM.c (Matrix_writeMatrixMarket): Added read/write routines
2315 :     for the Harwell-Boeing and the MatrixMarket formats.
2316 : maechler 834
2317 :     2005-08-04 Martin Maechler <maechler@stat.math.ethz.ch>
2318 :    
2319 :     * man/dtrMatrix-class.Rd: add examples
2320 : bates 835 * man/dtpMatrix-class.Rd: ditto; plus note about PROBLEM
2321 : maechler 834
2322 :     * TODO: note the dtpMatrix (docu) bug
2323 :    
2324 :     * R/zzz.R (.onLoad): assignInNamespace("as.matrix", *, "base")
2325 :     in order to ensure that new as.matrix() is used by old functions,
2326 :     e.g., svd(), qr(), eigen(), dist(),..;
2327 :     apply(), also matplot() or pairs().
2328 :    
2329 :    
2330 :     2005-08-03 Martin Maechler <maechler@stat.math.ethz.ch>
2331 :    
2332 :     * R/lmer.R: add 'fixme' comments and move the linear vs glm check;
2333 :     add comments about 'control' / lmerControl() arguments
2334 :    
2335 : bates 835 2005-07-27 Douglas Bates <bates@wisc.edu>
2336 : bates 820
2337 : bates 835 * man/sleepstudy.Rd: Added the sleep data set.
2338 : maechler 1174 * DESCRIPTION (Version): 0.98-1 released to CRAN
2339 : bates 820
2340 : bates 835 2005-07-12 Douglas Bates <bates@wisc.edu>
2341 : maechler 834 * man/sleepstudy.Rd: Added the sleep data set.
2342 :    
2343 : bates 809 * R/lmer.R (glmmMCMC): Added PACKAGE = "Matrix" in a couple of
2344 :     .Call calls that were producing spurious output.
2345 :    
2346 : bates 835 2005-07-05 Douglas Bates <bates@wisc.edu>
2347 : bates 801
2348 :     * R/lmer.R (lmer): stored updated variance component estimates in
2349 :     mer object for the generalized model. (Bug reported by Renaud
2350 :     Lancelot).
2351 :    
2352 : bates 835 2005-07-03 Douglas Bates <bates@wisc.edu>
2353 : bates 794
2354 :     * src/lmer.c (glmer_devAGQ): Added AGQ for single grouping factor,
2355 :     unidimensional case.
2356 :    
2357 : bates 835 2005-06-08 Douglas Bates <bates@wisc.edu>
2358 : maechler 791
2359 :     * DESCRIPTION (Version): 0.96-1
2360 :    
2361 : maechler 1174 * moved lmer-class' R and C code moved from lme4 to here
2362 : maechler 791
2363 : bates 835 2005-06-04 Douglas Bates <bates@wisc.edu>
2364 : bates 763
2365 :     * R/dgCMatrix.R: Call to csc_matrix_mm used undefined arguments
2366 :     (reported by Guissepe Ragusa <gragusa@ucsd.edu>)
2367 :    
2368 : bates 835 2005-06-02 Douglas Bates <bates@wisc.edu>
2369 : bates 763
2370 :     * src/Makefile.win: Forgot to update this when Makefile changed.
2371 :    
2372 : bates 835 2005-05-11 Douglas Bates <bates@wisc.edu>
2373 : bates 726
2374 :     * src/dgCMatrix.c (csc_transpose): Simplified function fixing a
2375 :     bug reported by Kurt Hornik and Michael Hahsler.
2376 :    
2377 : bates 835 2005-05-10 Douglas Bates <bates@wisc.edu>
2378 : bates 725
2379 :     * src/lgCMatrix.c (Matrix_lgClgCmm): Implementation of methods for
2380 :     logical sparse matrices. These will also be used in the symbolic
2381 :     analysis for lmer objects.
2382 :    
2383 :     * src/dsCMatrix.c (dsCMatrix_matrix_solve): Copied the dimensions
2384 :     of b to the result. Fixes bug reported by Jean.Coursol@math.u-psud.fr
2385 : maechler 791
2386 : bates 835 2005-05-06 Douglas Bates <bates@wisc.edu>
2387 : bates 714
2388 :     * src/dgeMatrix.c (dgeMatrix_colsums): Added an implementation of
2389 :     colMeans, colSums, rowMeans and rowSums.
2390 :    
2391 : bates 835 2005-04-18 Douglas Bates <bates@wisc.edu>
2392 : bates 692
2393 :     * src/lgCMatrix.[ch]: code for _validate method and stub for
2394 :     multiplication operation.
2395 :    
2396 :     * src/dgeMatrix.c (dgeMatrix_matrix_solve): Passing wrong argument
2397 :     to dgetrs.
2398 :    
2399 :     * src/init.c: Fix cut-and-paste error in definition of
2400 :     dgeMatrix_matrix_solve
2401 :    
2402 :     * src/{many files}: Tighten code by using ALLOC_SLOT.
2403 :    
2404 : bates 835 2005-04-15 Douglas Bates <bates@wisc.edu>
2405 : bates 692
2406 :     * R/AllClass.R: Add lgTMatrix and lgCMatrix classes
2407 :    
2408 :     * DESCRIPTION: Eliminate import of stats.
2409 :    
2410 : maechler 791
2411 : bates 835 2005-04-06 Douglas Bates <bates@wisc.edu>
2412 : bates 692
2413 :     * R/AllClass.R : add logical sparse matrix classes
2414 :    
2415 : maechler 687 2005-04-01 Martin Maechler <maechler@stat.math.ethz.ch>
2416 :    
2417 :     * R/dgTMatrix.R: add "[" method for triplet matrices
2418 :     * R/sparseMatrix.R: and other sparse ones; --> add show() for sparse
2419 :    
2420 : bates 835 2005-03-31 Douglas Bates <bates@wisc.edu>
2421 : maechler 687
2422 :     * DESCRIPTION (Version): release 0.95-5 to CRAN
2423 :    
2424 :     * R/dMatrix.R: add %*%, crossprod and solve "fallback" methods
2425 :     * R/sparseMatrix.R: %*%, crossprod()
2426 :     * R/dgeMatrix.R: more "fallback" methods for numeric/dense matrices
2427 :     * man/*.Rd: move method definitions to 'Matrix' and 'dMatrix'
2428 :     * src/lmer.c (lmer_fitted): fix thinko
2429 :    
2430 : maechler 676 2005-03-26 Martin Maechler <maechler@stat.math.ethz.ch>
2431 :    
2432 :     * R/AllClass.R: add two virtual sparse classes ``on top''
2433 :    
2434 :     2005-03-24 Martin Maechler <maechler@stat.math.ethz.ch>
2435 :    
2436 :     * R/AllClass.R (setClass): use "VIRTUAL" for the virtual classes;
2437 :     correspondingly fix examples and tests/ since new()
2438 :     doesn't work for virtual classes.
2439 :    
2440 : maechler 658 2005-03-17 Martin Maechler <maechler@stat.math.ethz.ch>
2441 :    
2442 :     * R/Matrix.R (as.matrix): method and one for unname()
2443 :     * tests/dpoMatrix.R: tests should now be less platform dependent;
2444 :     also run for R 2.1.0; using as.matrix()
2445 :    
2446 : bates 835 2005-03-15 Douglas Bates <bates@wisc.edu>
2447 : maechler 658
2448 :     * R/pMatrix.R: "pMatrix" class added
2449 :     * ....
2450 :    
2451 : bates 835 2005-03-14 Douglas Bates <bates@wisc.edu>
2452 : bates 645
2453 :     * R/dtpMatrix.R: Add unpack method and an example.
2454 :    
2455 :     * src/dsyMatrix.c (dsyMatrix_trf): Add BunchKaufman factorization
2456 :     of general symmetric matrices and associated S4 methods.
2457 :    
2458 : maechler 658 2005-03-10 Martin Maechler <maechler@stat.math.ethz.ch>
2459 :     +
2460 :     2005-03-05 Martin Maechler <maechler@stat.math.ethz.ch>
2461 :    
2462 :     * R/dgeMatrix.R (setAs): and many other files: more coercion,
2463 :     crossprod() and "%*%" methods added; tests, too.
2464 :     * tests/matprod.R: new, for testing these
2465 :    
2466 : bates 835 2005-03-03 Douglas Bates <bates@wisc.edu>
2467 : bates 599
2468 :     * src/lmer.c (lmer_fitted): Added.
2469 :    
2470 : bates 835 2005-03-02 Douglas Bates <bates@wisc.edu>
2471 : bates 596
2472 :     * R/dsTMatrix.R: Conversion from dsTMatrix to dsCMatrix
2473 :    
2474 : bates 835 2005-02-28 Douglas Bates <bates@wisc.edu>
2475 : bates 582
2476 :     * src/*.c,po/,inst/po: Internationalization and localization of
2477 :     the package.
2478 :    
2479 :     * src/ldl.[ch]: Removed these as their contents are referenced in the
2480 :     R_ldl.c file.
2481 :    
2482 :     * src/flame.[ch]: Removed these source files.
2483 : maechler 658
2484 : bates 582 * src/dtrMatrix.c (make_array_triangular): Move to Mutils
2485 :    
2486 :     * src/LU.[ch],src/init.c: absorb in factorizations
2487 :    
2488 :     * src/Mutils.h: prepare for internationalization
2489 :    
2490 :     * src/cblas.h: move the enum definitions to Mutils.h and remove
2491 :     this file
2492 :    
2493 : maechler 578 2005-02-26 Martin Maechler <maechler@stat.math.ethz.ch>
2494 :    
2495 : maechler 579 * R/dgeMatrix.R: provide "dimnames" and "dimnames<-" methods
2496 :    
2497 :     * R/dtrMatrix.R: fix t() method
2498 :    
2499 : maechler 578 * R/dgeMatrix.R: define group methods "Arith", "Math", "Math2"
2500 : maechler 658 * NAMESPACE: export them (and import generics from "methods")
2501 : maechler 578 * tests/group-methods.R : and test them.
2502 :    
2503 :     * src/dtrMatrix.c (dtrMatrix_as_dgeMatrix): prevent seg.fault in
2504 :     border case
2505 :    
2506 :     2005-02-24 Douglas Bates <bates@stat.wisc.edu>
2507 :    
2508 : maechler 658 * DESCRIPTION (Version): 0.95-2 released to CRAN
2509 : maechler 578
2510 :     * src/dgBCMatrix.c:
2511 :     * src/lmer.c: many changes
2512 :     * ...
2513 :    
2514 : maechler 512 2005-02-04 Martin Maechler <maechler@stat.math.ethz.ch>
2515 :    
2516 :     * R/Matrix.R: add more sophisticated show() method.
2517 :    
2518 : maechler 578 2005-02-02 Douglas Bates <bates@stat.wisc.edu>
2519 :    
2520 :     * */* : almost complete reorganization of classes.
2521 :    
2522 : bates 835 2005-01-26 Douglas Bates <bates@wisc.edu>
2523 : bates 460
2524 :     * R/AllGeneric.R: Added matrix exponential generic expm and a method
2525 :     for the geMatrix class.
2526 :    
2527 : bates 835 2005-01-24 Douglas Bates <bates@wisc.edu>
2528 : bates 460
2529 :     * src/Makefile (clean): Remove *.a and *.so
2530 :    
2531 :     * man/cscBlocked-class.Rd: Remove reference to the lmer-class.
2532 :    
2533 : bates 835 2005-01-23 Douglas Bates <bates@wisc.edu>
2534 : bates 460
2535 : maechler 658 * src/lmer.c (Lind): Definition of Lind was backwards. This only
2536 : bates 460 had an effect in cases with more than 2 grouping factors.
2537 :    
2538 : bates 835 2005-01-03 Douglas Bates <bates@wisc.edu>
2539 : bates 415
2540 :     * src/lmeRep.c (lmer_variances): change from lmeRep to lmer
2541 :    
2542 : bates 835 2004-12-23 Douglas Bates <bates@wisc.edu>
2543 : bates 410
2544 :     * src/init.c (R_init_Matrix): Reorder calls to R_registerRoutines
2545 :     and R_useDynamicSymbols (suggested by B.D.Ripley).
2546 :    
2547 : bates 835 2004-12-14 Douglas Bates <bates@wisc.edu>
2548 : bates 392
2549 :     * R/sscMatrix.R: Add determinant methods
2550 :    
2551 :     * src/triplet.[ch],src/init.c (triplet_to_matrix): Add a coercion
2552 :     for tripletMatrix to matrix.
2553 :    
2554 : bates 835 2004-12-13 Douglas Bates <bates@wisc.edu>
2555 : bates 388
2556 : bates 392 * R/AllClass.R (.onLoad): Eliminate the bbCrosstab class, which is
2557 :     no longer used.
2558 :    
2559 : bates 388 * src/R_ldl.c: Created an R-specific version of the ldl.[ch] files
2560 :     with dynamic allocation of scratch arrays.
2561 :    
2562 :     * src/ssclme.c (ssclme_copy_ctab): Fixed bug in creation of ZtZ
2563 :     for multivariate random effects with multiple grouping factors.
2564 :     Fixes part but not all of #15.
2565 :    
2566 : bates 835 2004-12-03 Douglas Bates <bates@wisc.edu>
2567 : bates 375
2568 :     * src/lmeRep.c (lmeRep_factor): order of operations for multiple
2569 :     scalar grouping factors corrected.
2570 :    
2571 : bates 835 2004-11-29 Douglas Bates <bates@wisc.edu>
2572 : bates 375
2573 :     * src/bCrosstab.c: remove diag_update which is no longer used
2574 :    
2575 : bates 835 2004-11-16 Douglas Bates <bates@wisc.edu>
2576 : bates 350
2577 :     * src/Metis_utils.c: Move metis.h include to C sources so that the
2578 :     .h file can be included.
2579 :    
2580 : bates 835 2004-11-12 Douglas Bates <bates@wisc.edu>
2581 : bates 342
2582 : bates 350 * src/LU.c,geMatrix.c,trMatrix.c, etc.:
2583 : bates 342 Complete allocation of slots in NEW_OBJECT.
2584 :    
2585 :     * src/Mutils.h: Moved list of symbols to an include file
2586 :    
2587 : bates 835 2004-11-11 Douglas Bates <bates@wisc.edu>
2588 : bates 342
2589 :     * src/geMutils.c (Matrix_init): remove unused function
2590 :    
2591 : bates 835 2004-11-10 Douglas Bates <bates@wisc.edu>
2592 : bates 342
2593 :     * src/cscMatrix.c (csc_to_imagemat): removed unused function
2594 :    
2595 : bates 835 2004-11-05 Douglas Bates <bates@wisc.edu>
2596 : bates 327
2597 :     * src/Makefile.win (SOURCES_C): Keep consistent with Makefile
2598 :    
2599 : bates 835 2004-10-27 Douglas Bates <bates@wisc.edu>
2600 : bates 303
2601 :     * R/pdmatrix.R: remove PACKAGE="Matrix" in .Call calls
2602 :    
2603 : bates 835 2004-10-04 Douglas Bates <bates@wisc.edu>
2604 : bates 296
2605 :     * src/init.c: Created R_init_Matrix and added registration of C
2606 :     routines.
2607 :    
2608 : bates 835 2004-10-02 Douglas Bates <bates@wisc.edu>
2609 : bates 283
2610 :     * R/tripletMatrix.R: Force a require(lattice) for the image methods.
2611 :    
2612 : bates 835 2004-06-15 Douglas Bates <bates@wisc.edu>
2613 : bates 229
2614 :     * man/trMatrix-class.Rd: Escape the % chars in .Rd files.
2615 :    
2616 : bates 111 2004-04-20 Douglas Bates <bates@stat.wisc.edu>
2617 :    
2618 :     * src/Makefile.win ($(SHLIB)): Modifications per Uwe Ligges.
2619 :    
2620 : bates 109 2004-04-19 Douglas Bates <bates@stat.wisc.edu>
2621 :    
2622 :     * src/ssclme.c (ssclme_update_mm): fix logic error in
2623 :     ssclme_update_mm
2624 :    
2625 : bates 105 2004-04-18 Douglas Bates <bates@stat.wisc.edu>
2626 :    
2627 :     * src/ssclme.c (ssclme_coef, ssclme_coefGets): Create consistency
2628 :     in the order of unconstrained and constrained parameters.
2629 :     (ssclme_gradient): Added the gradients (not yet correct for
2630 :     multidimensional, unconstrained case).
2631 :    
2632 : bates 78 2004-04-14 Douglas Bates <bates@stat.wisc.edu>
2633 :    
2634 :     * src/ssclme.c (ssclme_EMsteps): Fix logic in REML update
2635 :    
2636 :     * src/Makefile.win: Remove unneeded ranlib call
2637 :    
2638 : bates 71 2004-04-12 Douglas Bates <bates@stat.wisc.edu>
2639 :    
2640 :     * DESCRIPTION (Version): New release
2641 :    
2642 :     * src/Makefile.win: Update Makefile.win to umfpack removal.
2643 :    
2644 : bates 49 2004-04-05 Douglas Bates <bates@bates2_home>
2645 :    
2646 :     * src/triplet_to_col.c: Create triplet_to_col as a native
2647 : maechler 658 function, not the version from umfpack. There were problems with
2648 : bates 49 the configuration of UMFPACK for 64-bit processors and there was
2649 :     only one umfpack routine being used so I moved it here.
2650 :    
2651 : bates 45 2004-04-04 Douglas Bates <bates@bates2_home>
2652 :    
2653 :     * src/ssclme.c (ssclme_variances): New function.
2654 :    
2655 : bates 28 2004-03-28 Douglas Bates <bates@bates2_home>
2656 :    
2657 :     * src/ssclme.c (ssclme_fitted): Added function.
2658 :    
2659 : bates 22 2004-03-27 Douglas Bates <bates@bates2_home>
2660 :    
2661 :     * src/ssclme.c (ssclme_transfer_dimnames): Add new function to
2662 :     store the dimnames in the XtX and bVar slots
2663 :     (ssclme_update_mm): Change the dimensions of the bVar slot
2664 :     components and the returned value from ssclme_ranef.
2665 :    
2666 : bates 10 2004-03-18 Douglas Bates <bates@stat.wisc.edu>
2667 :    
2668 :     * R/{pdMat.R,pdIdent.R,pdLogChol.R,pdMatrixLog.R,pdNatural.R},
2669 :     src/{pdMat.c,pdIdent.c,pdLogChol.c,pdNatural.c},
2670 :     tests/{pdCompSymm.R,pdDiag.R,pdIdent.R,pdLogChol.R,pdNatural.R},
2671 :     man/{pdMat-class.Rd,pdmatrix-class.Rd,corrmatrix-class.Rd,
2672 :     pdDiag-class.Rd,pdIdent-class.Rd,pdNatural-class.Rd,
2673 :     pdLogChol-class.Rd,coefGets.Rd,pdCompSymm-class.Rd,
2674 :     pdfactor-class.Rd,pdFactor.Rd,pdMatrix.Rd,
2675 :     pdBlocked-class.Rd},AllClass.R,AllGeneric.R:
2676 :     Moved the pdMat classes from the lme4 package.
2677 :    
2678 :     2004-03-02 Douglas Bates <bates@stat.wisc.edu>
2679 :    
2680 :     * man/ssclme-class.Rd: Update definition and documentation of the
2681 :     ssclme class to include the DIsqrt slot.
2682 :    
2683 :     * src/ssclme.c (ssclme_deviance): Modify order of computation
2684 :     (much faster using dsyrk, a level 3 BLAS routine).
2685 :    
2686 :     * src/Makefile (SUBLIBS): Change definition (K. Hornik)
2687 :    
2688 :     2004-02-28 Douglas Bates <bates@stat.wisc.edu>
2689 :    
2690 :     * tests/ssclme.R: Modify the test to account for the permutation
2691 :     of the levels of the grouping factors.
2692 :    
2693 :     2004-02-23 Douglas Bates <bates@stat.wisc.edu>
2694 :    
2695 :     * R/ssclme.R,src/ssclme.c (ssclme): Move slots of sscCrosstab slot
2696 :     directly into the ssclme class definition.
2697 :    
2698 :     2004-02-22 Douglas Bates <bates@stat.wisc.edu>
2699 :    
2700 :     * DESCRIPTION (Date): New release
2701 :    
2702 :     * man/ssclme-class.Rd: new file.
2703 :    
2704 :     * src/ssclme.c (ssclme_loglik): major revisions in design. It
2705 :     works and it's fast!
2706 :    
2707 :     2004-02-17 Douglas Bates <bates@stat.wisc.edu>
2708 :    
2709 :     * src/taucs/Makefile.win (lib): Change "ar" to "$(AR)" (B.Ripley)
2710 :    
2711 :     2004-02-16 Douglas Bates <bates@stat.wisc.edu>
2712 :    
2713 :     * DESCRIPTION (Date): New release
2714 :    
2715 :     * NAMESPACE: Don't export ssclme.
2716 :    
2717 :     * data/ScotsSec.rda, man/ScotsSec.Rd: Add Scottish secondary
2718 :     school data.
2719 :    
2720 :     2004-02-11 Douglas Bates <bates@stat.wisc.edu>
2721 :    
2722 :     * src/sscCrosstab.c (sscCrosstab): Added a row to the incidence to
2723 :     keep track of the fixed-effects and the response. Counts also
2724 :     gets an extra element, which is always one.
2725 :    
2726 :     * src/ldl.c: Include these routines from Tim Davis' LDL package.
2727 :    
2728 :     2004-02-10 Douglas Bates <bates@stat.wisc.edu>
2729 :    
2730 :     * src/cscMatrix.c (csc_transpose): new function
2731 :    
2732 :     * src/Mutils.c (csc_sort_columns): perm/iperm confusion corrected
2733 :     (csc_components_transpose): new function
2734 :    
2735 :     2004-02-06 Douglas Bates <bates@stat.wisc.edu>
2736 :    
2737 :     * src/triplet.c (triplet_validate): Fix Dim slot on generated
2738 :     triplets
2739 :    
2740 :     2004-01-30 Douglas Bates <bates@stat.wisc.edu>
2741 :    
2742 :     * R/sscCrosstab.R (sscCrosstab): Added sscCrosstab generator function.
2743 :    
2744 :     * src/LU.h (MATRIX_LU_H): Add #ifndef #define ... #endif to this
2745 :     and all other .h files in src.
2746 :    
2747 :     * src/Makefile.win: This and other Makefile.win files contributed
2748 :     by Brian Ripley.
2749 :    
2750 :     2004-01-27 Douglas Bates <bates@stat.wisc.edu>
2751 :    
2752 :     * R/syMatrix.R: Added methods for "%*%".
2753 :    
2754 :     * R/Hilbert.R (Hilbert): Changed Hilbert function to return a
2755 :     poMatrix object.
2756 :    
2757 :     2004-01-26 Douglas Bates <bates@stat.wisc.edu>
2758 :    
2759 :     * man/sscChol-class.Rd,man/mm.Rd,man/y.Rd: Added man pages.
2760 :    
2761 :     2004-01-25 Douglas Bates <bates@bates2_home>
2762 :    
2763 :     * inst/doc/Introduction.Rnw,Comparisons.Rnw: Added vignettes.
2764 :    
2765 :     * R/csc.R: Convert all cscMatrix classes to use Dim slot instead
2766 :     of nrow.
2767 :    
2768 :     2003-12-31 Douglas Bates <bates@stat.wisc.edu>
2769 :    
2770 :     * src/taucs/taucs.h: Moved taucs.h, amd.h, and umfpack.h into
2771 :     subdirectories.
2772 :    
2773 :     2003-12-08 Douglas Bates <bates@stat.wisc.edu>
2774 :    
2775 :     * src/taucs.h: Accidently referred to global header files
2776 :     instead of local files.
2777 :    
2778 :     2003-12-04 Douglas Bates <bates@stat.wisc.edu>
2779 :    
2780 :     * R/AllClass.R: Lots of changes. Removed all the lapack++ code
2781 :     and methods and replaced all classes with S4 classes.
2782 :    
2783 :     2003-04-19 Douglas Bates <bates@stat.wisc.edu>
2784 :    
2785 :     * R/det.R,man/det.Rd: Change name of det generic to determinant
2786 :    
2787 :     * src/R_LapackPP.cc: Change method of calculating determinants
2788 :    
2789 :     2003-02-03 Douglas Bates <bates@stat.wisc.edu>
2790 :    
2791 :     * DESCRIPTION (Version): removed empty data directory as requested
2792 :     by CRAN maintainers. Changed version number and date.
2793 :    
2794 :     2002-10-23 Douglas Bates <bates@stat.wisc.edu>
2795 :    
2796 :     * src/laindex.h: Applied patches from Brian Ripley for compilation
2797 :     under Windows.
2798 :    
2799 :     * Added configure.win and src/Makevars.win as requested by Brian
2800 :     Ripley.
2801 :    
2802 :     2002-05-03 Douglas Bates <bates@stat.wisc.edu>
2803 :    
2804 :     * src/lamatrix.h: Removing pre-1.2.0 compatibility code per Kurt
2805 :     Hornik.
2806 :    
2807 :     2002-04-24 Douglas Bates <bates@stat.wisc.edu>
2808 :    
2809 :     * configure.ac: Replaced configure.in with configure.ac
2810 :     contributed by Kurt Hornik.
2811 :    
2812 :     * aclocal.m4 (ac_clean_files): Replaced this with Kurt Hornik's
2813 :     version for R-1.5.0
2814 :    
2815 : maechler 512
2816 : bates 10 2001-12-10 Douglas Bates <bates@stat.wisc.edu>
2817 :    
2818 :     * man/eigen.Rd: Removed the .Alias in the example

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