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Annotation of /pkg/ChangeLog

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

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