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Annotation of /pkg/ChangeLog

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Revision 2166 - (view) (download)

1 : maechler 2166 2008-04-02 Martin Maechler <maechler@stat.math.ethz.ch>
2 :    
3 :     * src/dense.c (dense_to_Csparse): all declarations *before*
4 :     R_CheckStack(); needed e.g. for ancient gcc 2.96.
5 :    
6 :    
7 : maechler 2159 2008-03-29 Martin Maechler <maechler@stat.math.ethz.ch>
8 :    
9 :     * DESCRIPTION (Version): 0.999375-9 --- need to release
10 :     for R-devel (and R 2.7.0 alpha soon).
11 :    
12 : maechler 2165 * R/AllClass.R: drop "double" from "atomicVector" class union
13 :    
14 : maechler 2161 * R/AllGeneric.R (rcond): check for base::rcond instead of R version
15 : maechler 2164 * R/dgeMatrix.R: ditto
16 : maechler 2161
17 : maechler 2159 * R/sparseMatrix.R (summary): count NAs
18 :    
19 : maechler 2165 * inst/doc/Intro2Matrix.Rnw: changes, aim for *one* introduction.
20 :    
21 : maechler 2158 2008-03-28 Martin Maechler <maechler@stat.math.ethz.ch>
22 :    
23 :     * R/AllGeneric.R: rcond(., norm) instead of rcond(., type), in
24 :     order to become compatible to new R 2.7.0 base::rcond().
25 :    
26 : maechler 2157 2008-03-25 Martin Maechler <maechler@stat.math.ethz.ch>
27 :    
28 : maechler 2158 * DESCRIPTION (Version,Date): 0.999375-8 --- released to CRAN
29 : maechler 2157
30 :     * R/diagMatrix.R (Ops): fix newly introduce bug in <.di> o <numeric>
31 :    
32 :     * inst/test-tools.R (isValid): new utility, used much in
33 :     * tests/simple.R:
34 :    
35 :     * man/BunchKaufman-methods.Rd: added too
36 :    
37 :     2008-03-24 Martin Maechler <maechler@stat.math.ethz.ch>
38 :    
39 :     * R/dsyMatrix.R: add BunchKaufman() methods.
40 :     * R/dspMatrix.R:
41 :    
42 :     * src/init.c: add dsyMatrix_trf
43 :    
44 :     2008-03-23 Douglas Bates <bates@stat.wisc.edu>
45 :    
46 :     * DESCRIPTION (Version): release 0.999375-7
47 :     * src/CHMfactor.c (CHMfactor_update): fix
48 :    
49 : maechler 2154 2008-03-22 Martin Maechler <maechler@stat.math.ethz.ch>
50 :    
51 :     * src/dsCMatrix.c (dsCMatrix_LDL_D): cleanup, also using
52 :     internal_chm_factor().
53 :    
54 :     * R/AllGeneric.R: do *not* define a "chol" generic
55 :     (but rather use the implicit one *without* making pivot
56 :     part of the signature)
57 :     * R/*.R: drop the 'pivot' from chol's signature and make
58 :     'pivot=FALSE' a default argument of method definitions.
59 :    
60 :     * .Rbuildignore: add 'wrld_1deg': I.e. do not put it into released
61 :     version of Matrix
62 :    
63 : maechler 2139 2008-03-18 Martin Maechler <maechler@stat.math.ethz.ch>
64 :    
65 : maechler 2144 * R/Tsparse.R (.T.2.n): drop 0's before coercion to "nMatrix"
66 :    
67 :     * R/sparseMatrix.R (is.na): new simple method
68 :     * R/denseMatrix.R (is.na): ditto.
69 :    
70 :     * R/diagMatrix.R (.symDiagonal): newly exported utility.
71 :    
72 :     * R/diagMatrix.R (Ops): <diag> * <numeric> should not become dgeMatrix!
73 :    
74 : maechler 2139 * src/UFsparse_download.sh: -->
75 :     * src/CHOLMOD/: update to CHOLMOD version 1.6 (Nov.2007)
76 :    
77 : maechler 2137 2008-03-17 Martin Maechler <maechler@stat.math.ethz.ch>
78 :    
79 :     * src/dsCMatrix.c (dsCMatrix_LDL_D): even faster utility with same
80 :     functionality; barely tested in
81 :     * tests/factorizing.R
82 :    
83 :     * src/Csparse.c (diag_tC): new functionality to enable faster
84 :     determinant(<dsCMatrix>, .) in
85 :     * R/dsCMatrix.R
86 :    
87 :     2008-03-17 18:53 Douglas Bates <bates@stat.wisc.edu>
88 :    
89 :     * R/CHMfactor.R, inst/include/Matrix.h, inst/include/Matrix_stubs.c,
90 :     src/CHMfactor.c, src/CHMfactor.h,
91 :     man/CHMfactor-class.Rd, src/init.c, tests/factorizing.R:
92 :     Log-determinant of the parent matrix from a CHMfactor object as
93 :     chm_factor_ldetL2; documentation and support
94 :    
95 :     2008-03-15 Martin Maechler <maechler@stat.math.ethz.ch>
96 :    
97 :     * R/dsCMatrix.R: enable determinant(<dsCMatrix>, .) via chol(.)
98 :    
99 : maechler 2130 2008-03-14 Martin Maechler <maechler@stat.math.ethz.ch>
100 :    
101 :     * R/dsCMatrix.R: setAs(., "dsCMatrix") but with a deprecation
102 :     warning.
103 :    
104 : maechler 2128 2008-03-13 Martin Maechler <maechler@stat.math.ethz.ch>
105 :    
106 :     * DESCRIPTION (Version, Date): bug-fix release 0.999375-6
107 :    
108 :     * R/diagMatrix.R (diag2tT.u): utility to be smarter in
109 :     <diagonal> o <sparse_triangular>
110 :     setAs(., "nMatrix") added.
111 :    
112 :     * R/diagMatrix.R (Diagonal): Diagonal(4, x=3) now works too
113 :    
114 :     * R/Auxiliaries.R (.diagU2N): more careful coercion in 2 steps
115 :     new argument 'checkDense = FALSE'.
116 :    
117 :    
118 : maechler 2125 2008-03-07 Martin Maechler <maechler@stat.math.ethz.ch>
119 :    
120 : maechler 2127 * src/dgeMatrix.c (dgeMatrix_exp): fix the octave-origin bug in the
121 :     back-permutation of the matrix exponential.
122 :    
123 :     * tests/matr-exp.R: test the fix (for an example where expm() was wrong).
124 :    
125 : maechler 2126 * DESCRIPTION (Date,Version): ready to release 0.999375-5
126 :    
127 : maechler 2125 * tests/simple.R: testing diagN2U
128 :    
129 :     2008-03-06 Martin Maechler <maechler@stat.math.ethz.ch>
130 :    
131 :     * R/Auxiliaries.R (diagN2U): interface to
132 :    
133 :     * src/Csparse.c (Csparse_diagN2U): .Call()able SEXP version of chm_diagN2U()
134 :    
135 :     * tests/matprod.R: test for triangularity preserving <dtC> %*% <dtC>
136 :    
137 : maechler 2123 2008-03-05 Martin Maechler <maechler@stat.math.ethz.ch>
138 :    
139 : maechler 2125 * src/chm_common.c (chm_diagN2U): new utility.
140 :    
141 :     * src/Csparse.c (Csparse_Csparse_crossprod, Csparse_Csparse_prod):
142 :     make use of chm_diagN2U() and hence now preserve triangularity and
143 :     unit-triangularity.
144 :    
145 : maechler 2123 * DESCRIPTION (LicenseDetails): new; such that 'License:' becomes "canonical"
146 :    
147 : maechler 2120 2008-03-04 Martin Maechler <maechler@stat.math.ethz.ch>
148 :    
149 :     * R/diagMatrix.R (subDiag): fix when x[..] became a vector
150 :    
151 :     * src/Tsparse.c (Tsparse_diagU2N): new utility, necessary for e.g.
152 :     * src/Csparse.c (Csparse_crossprod): use [CT]sparse_diagU2N() !!
153 :    
154 :     * R/Auxiliaries.R (.diagU2N): make use of new Tsparse_diagU2N
155 :    
156 :     * R/Ops.R ("-" (<sparseMatrix>)): use diagU2N()
157 :    
158 :     * src/chm_common.c (AS_CHM_FINISH): add note about problem
159 :     for triangular (diag = "U").
160 :    
161 : maechler 2115 2008-02-21 Martin Maechler <maechler@stat.math.ethz.ch>
162 :    
163 :     * R/Auxiliaries.R (as_Csparse2): drop this, replacing by
164 :     * R/bind.R: .Call(dense_to_Csparse, *)
165 :    
166 :     2008-02-20 Martin Maechler <maechler@stat.math.ethz.ch>
167 :    
168 :     * R/Matrix.R (Matrix): no longer use coercions to specific classes
169 :     (since we are discouraging them in user code).
170 :    
171 :     * tests/*.R: also replaces coercions to specific classes by
172 :     coercions to super classes.
173 :    
174 :     * R/denseMatrix.R (.dense2C): simplified by using forceSymmetric()
175 :    
176 :    
177 :     2008-02-19 Martin Maechler <maechler@stat.math.ethz.ch>
178 :    
179 :     * man/CAex.Rd: example: coerce to symmetric*, not dsC*
180 :    
181 :     * src/dense.c (dense_band): generalized from ddense_band
182 :    
183 :     * R/ddenseMatrix.R (.trilDense,.triuDense, .bandDense):
184 :     now for "denseMatrix" (instead of just "ddense*"); much
185 :     simplified setMethod()s for these.
186 :    
187 :     * src/dense.c (dense_to_symmetric): generalized from ddense_*
188 :    
189 :     2008-02-18 Martin Maechler <maechler@stat.math.ethz.ch>
190 :    
191 :     * R/AllGeneric.R: forceSymmetric() generic: fast no-checking
192 :     version of as(*, "symmetricMatric").
193 :    
194 :     * src/dense.c (ddense_to_symmetric): add 'symm_test' argument, and
195 :     * R/symmetricMatrix.R: set it TRUE in coercion to "symmetricMatrix"
196 :    
197 : maechler 2113 2008-02-16 Martin Maechler <maechler@stat.math.ethz.ch>
198 :    
199 :     * R/Matrix.R (subset.ij): utility, as first step to faster
200 :     M [ <ij-matrix> ] indexing.
201 :    
202 :     * R/Matrix.R (.M.sub.i.logical): M[ <logical> ] : try better.
203 :    
204 :     * src/dense.c (ddense_symmpart, ddense_skewpart): new functions
205 :     for more efficient symmpart() and skewpart() methods.
206 :    
207 :     * src/Mutils.c (equal_string_vectors): utility
208 :    
209 :     * src/dense.c (ddense_to_symmetric): new function used in
210 :    
211 :     * R/symmetricMatrix.R: setAs(., "symmetricMatrix")
212 :    
213 :     * R/sparseMatrix.R, et_al (isSymmetric): add '...' to formals, in
214 :     order to match the generic (and evade .local(..)).
215 :    
216 :     * R/dsCMatrix.R: dgC -> dsC: use C code!
217 :    
218 :     * NAMESPACE, R/AllGeneric.R (symmpart, skewpart): new functions
219 :     as per TODO
220 :    
221 :     * R/Auxiliaries.R (setZero, all0Matrix): new utilities
222 :    
223 :     * R/symmetricMatrix.R: obvious symmpart(), skewpart() methods
224 :    
225 :    
226 :     2008-02-15 Martin Maechler <maechler@stat.math.ethz.ch>
227 :    
228 :     * R/Ops.R (.Arith.Csparse): use diagU2N when needed in triangular
229 :    
230 :     * R/Auxiliaries.R (non0.i): take out of non0ind
231 :    
232 :     * R/ddenseMatrix.R (.trilDense, .triuDense, .bandDense):
233 :     make tril(), triu(), band() work for "matrix" and all "dense*"
234 :    
235 :     * R/triangularMatrix.R (.tri[lu].tr): need .diagU2N(*)
236 :     * tests/simple.R: test the fix above
237 :    
238 :     * R/sparseMatrix.R ([): simplification: no coerce to <general>
239 :     before we use as(., <Tsparse>)[...] anyway
240 :    
241 :     * R/Rsparse.R (.viaC.to.R): mostly instead of .viaC.to.dgR()
242 :    
243 :     * R/triangularMatrix.R (isTriangular): methods for all subclasses
244 :     instead of "triangularMatrix" -- just to disambiguate
245 :    
246 :     2008-02-14 Martin Maechler <maechler@stat.math.ethz.ch>
247 :    
248 :     * tests/Class+Meth.R (dotestMat): add m[FALSE, FALSE] { <-> TODO}
249 :     * tests/indexing.R: example that fails above
250 :    
251 : maechler 2110 2008-01-26 Martin Maechler <maechler@stat.math.ethz.ch>
252 :    
253 :     * R/Matrix.R (.M.sub.i.2col): fix for logical matrix indexing
254 :     * R/Tsparse.R (.TM.sub.i.2col, .TM.repl.i.2col): ditto;
255 :     now, M[lower.tri(M)] and M[lower.tri(M)] <- v work better
256 :    
257 :     * src/Tsparse.c (Tsparse_to_tCsparse): new fast utility.
258 :     * src/Tsparse.h, init.c: ditto
259 :     * R/Auxiliaries.R (isTriT): new; faster than going via Csparse
260 :     both isTriC() and isTriT() now return TRUE with "kind" or FALSE.
261 :     * R/sparseMatrix.R (isTriangular): hence simplified
262 :    
263 : maechler 2108 2008-01-24 Martin Maechler <maechler@stat.math.ethz.ch>
264 :    
265 :     * R/Ops.R (.Arith.Csparse): new utility factored out of former
266 :     <dgC> o <dgC>, extended for triangular and also used in <dtC> o <dtC>.
267 :    
268 : maechler 2106 2008-01-23 Martin Maechler <maechler@stat.math.ethz.ch>
269 :    
270 :     * tests/factorizing.R (checkSchur): and more tests for checking Schur()
271 :    
272 : maechler 2108 * inst/test-tools.R (isOrthogonal): new function; also file restructured
273 : maechler 2106
274 :     2008-01-22 Martin Maechler <maechler@stat.math.ethz.ch>
275 :    
276 :     * R/ngTMatrix.R: allow as(<numeric matrix>, "ngTMatrix") and hence
277 :     coercion to "nMatrix" and "pMatrix"
278 :    
279 :     * R/AllClass.R: "Schur" class; "number" class union
280 :     * man/number-class.Rd:
281 :     * man/Schur-class.Rd:
282 :    
283 :     * R/eigen.R (.dgeSchur): utility, and return "Schur" class
284 :     (.simpleSchur): Schur() method for diagonal matrices
285 :     (.triSchur): Schur() method for triangular matrices
286 :     (Schur.sym): Schur() for symmetric matrices {building on eigen()}.
287 :    
288 :    
289 :     2008-01-21 Martin Maechler <maechler@stat.math.ethz.ch>
290 :    
291 :     * src/dgCMatrix.c (dgCMatrix_QR): set @Dim slot (as per doc)
292 :    
293 : maechler 2105 2008-01-15 Martin Maechler <maechler@stat.math.ethz.ch>
294 :    
295 :     * R/CHMfactor.R (solve): method for b="numeric", but also b="ANY"
296 :     in order to ensure 'system = *' is not lost;
297 :     formals()$system instead of cut&paste.
298 :     * tests/factorizing.R: test solve(<CHM..>, <numeric>)
299 :    
300 : maechler 2102 2008-01-11 Martin Maechler <maechler@stat.math.ethz.ch>
301 : maechler 2096
302 : maechler 2105 * DESCRIPTION (Date): make ready for release --> 0.999375-4
303 : maechler 2096
304 : maechler 2102 * R/dgeMatrix.R: fix rcond() method for "dgeMatrix".
305 : maechler 2096
306 : maechler 2098 2007-12-08 Martin Maechler <maechler@stat.math.ethz.ch>
307 : maechler 2096
308 : maechler 2098 * R/pMatrix.R: as(*, "matrix") now returns 0/1 *integer* matrix,
309 :     and hence does as.vector(.).
310 :     * man/pMatrix-class.Rd: docs
311 :     * R/sparseMatrix.R: fix for printing "integer sparse"
312 :    
313 :     * tests/Class+Meth.R (tstMatrixClass): test M[FALSE], M[2] etc
314 :    
315 :     * R/Matrix.R and others: use "exact" function argument list for
316 :     both "[" : (x, i,j, ..., drop)
317 :     and "[<-" : (x, i,j, ..., value)
318 :    
319 :     * R/denseMatrix.R: M[i] and M[i] <- v (i vector) now work
320 :     * R/Tsparse.R (replTmat): ditto
321 :     * R/diagMatrix.R (replDiag): ditto
322 :     * R/Csparse.R (replCmat): ditto {was it worth the pain?}
323 :     * tests/indexing.R: testing the above
324 :    
325 : maechler 2096 2007-12-07 Martin Maechler <maechler@stat.math.ethz.ch>
326 :    
327 :     * R/sparseMatrix.R (cov2cor): method for sparse matrices
328 :    
329 :     * R/diagMatrix.R ([<-): fix D[ cbind(i,j) ] <- v
330 :    
331 :     * R/bind2.R: fix for Rsparse* and rbind2(dense,dense)
332 :    
333 :     * tests/Class+Meth.R: test cbind2, rbind2 and diag<-
334 :    
335 :     2007-12-06 Martin Maechler <maechler@stat.math.ethz.ch>
336 :    
337 :     * R/Matrix.R: "generic" cov2cor() method
338 :    
339 :     * R/nearPD.R: new 'only.values', 'keepDiag' arguments;
340 :     speed up Q %*% D %*% t(Q)
341 :     * tests/dpoMatrix.R: test nearPD()
342 :    
343 :     2007-12-05 Doug Bates and Martin Maechler
344 :    
345 :     * R/sparseMatrix.R: xtabs(*, sparse=.) function; an extention of
346 :     stats::xtabs() allowing to create sparse matrices.
347 :    
348 :     2007-10-08 Martin Maechler <maechler@stat.math.ethz.ch>
349 :    
350 :     * DESCRIPTION (Version): *-4 (released *-3 two days ago)
351 :    
352 : maechler 2081 2007-10-06 Martin Maechler <maechler@stat.math.ethz.ch>
353 :    
354 :     * R/pMatrix.R: solve(<Matrix>, <pMatrix>)
355 :    
356 :     2007-10-05 Martin Maechler <maechler@stat.math.ethz.ch>
357 :    
358 :     * R/LU.R: solve() method for "denseLU"
359 :    
360 :     2007-10-01 Martin Maechler <maechler@stat.math.ethz.ch>
361 :    
362 :     * DESCRIPTION (Version): 0.999375-3 preparing for release
363 :    
364 :     * R/AllGeneric.R: simplify if(.) .. else .. for R <= 2.5.1
365 :    
366 :     * R/Matrix.R (Matrix): .Internal(matrix(..)) different for R >= 2.7.0
367 :    
368 : maechler 2073 2007-09-26 Martin Maechler <maechler@stat.math.ethz.ch>
369 :    
370 :     * R/pMatrix.R (.m.mult.pMat): fix <matrix> %*% <pMatrix>,
371 :     thanks to Kasper Kristensen.
372 :     * tests/matprod.R: regression test for that.
373 :    
374 : bates 2069 2007-09-23 17:32 Douglas Bates <bates@stat.wisc.edu>
375 :    
376 :     * [r4778] R/AllGeneric.R: Check R version before defining generics for
377 :     primitives
378 :    
379 : maechler 2073 2007-09-13 Martin Maechler <maechler@stat.math.ethz.ch>
380 :    
381 :     * R/denseMatrix.R (rcond): method
382 :     * R/sparseQR.R (rcond): method, use x or t(x)
383 :    
384 :     2007-09-12 Martin Maechler <maechler@stat.math.ethz.ch>
385 :    
386 :     * R/dgeMatrix.R (rcond): method: work via qr.R() for non-square
387 :     matrices.
388 :     * R/sparseMatrix.R: Ditto for all other rcond() method definitions.
389 :    
390 :     * man/rcond.Rd: mention the more general definition, and add
391 :     example for non-square matrices.
392 :    
393 :     * man/chol.Rd: new file, for the S4 chol() generic and all methods.
394 :    
395 :     2007-09-11 Martin Maechler <maechler@stat.math.ethz.ch>
396 :    
397 :     * R/sparseQR.R: add qr.R() method [to be used for rcond()]
398 :    
399 : maechler 2062 2007-09-01 Martin Maechler <maechler@stat.math.ethz.ch>
400 :    
401 :     * R/Matrix.R ([<-): add (Matrix,missing,ANY,Matrix) etc
402 :     * tests/indexing.R: add new regression for the above cases.
403 :    
404 : maechler 2061 2007-08-30 Martin Maechler <maechler@stat.math.ethz.ch>
405 :    
406 :     * src/Mutils.h (__sun): clause for alloca.h on Solaris
407 :    
408 : maechler 2056 2007-08-16 Martin Maechler <maechler@stat.math.ethz.ch>
409 :    
410 :     * DESCRIPTION (Date, Version): 0.999375-2
411 :    
412 :     2007-08-15 Martin Maechler <maechler@stat.math.ethz.ch>
413 :    
414 :     * R/HBMM.R (readMM): make work for pattern matrices as well
415 :    
416 : bates 2050 2007-08-14 13:07 Douglas Bates <bates@stat.wisc.edu>
417 :    
418 :     * [r4730] src/Mutils.h: declare alloca
419 :     * [r4734] NAMESPACE, R/AllGeneric.R, R/Csparse.R, R/HBMM.R, R/Tsparse.R,
420 :     R/dgCMatrix.R, R/dgTMatrix.R, R/dsCMatrix.R, R/dsTMatrix.R,
421 :     man/externalFormats.Rd, src/Csparse.c, src/Csparse.h, src/DEPS.mkf,
422 :     src/HBMM.c, src/HBMM.h, src/Mutils.h, src/SOURCES_C.mkf, src/init.c,
423 :     src/mmio.c, src/mmio.h: Remove deprecated function writeHB and its
424 :     methods; switch writeMM to use CHOLMOD code; repair readMM
425 :    
426 : maechler 2048 2007-08-14 Martin Maechler <maechler@stat.math.ethz.ch>
427 :    
428 :     * R/nearPD.R, man/nearPD.Rd (nearPD): new function built on Jens
429 :     Oehlschlaegel's ... result type still to be discussed!
430 :    
431 : maechler 2043 2007-08-10 Martin Maechler <maechler@stat.math.ethz.ch>
432 :    
433 :     * man/image-methods.Rd: new, combining all image() methods
434 :    
435 :     2007-08-09 Martin Maechler <maechler@stat.math.ethz.ch>
436 :    
437 :     * R/dgCMatrix.R: define qr() and lu() methods for "sparseMatrix"
438 :     to work via dgC...
439 :    
440 :     * R/Matrix.R (Matrix): special treatment for "table" (S3)
441 :    
442 :     2007-08-07 Martin Maechler <maechler@stat.math.ethz.ch>
443 :    
444 :     * R/dgTMatrix.R (image): change defaults to
445 :     aspect = "iso", colorkey = FALSE
446 :    
447 : maechler 2039 2007-08-06 Martin Maechler <maechler@stat.math.ethz.ch>
448 :    
449 :     * src/dsyMatrix.c (dsyMatrix_matrix_mm): 'b' might be matrix;
450 :     must copy its *expanded* x slot before LAPACK call.
451 :    
452 :     * tests/matprod.R: test the last days' changes.
453 :    
454 : bates 2041 2007-08-06 16:43 Douglas Bates <bates@stat.wisc.edu>
455 :    
456 :     * [r4712] inst/include/Matrix_stubs.c: Change R_cholmod_printf in stubs
457 :     as well as in sources
458 : bates 2050 * [r4713] src/dsyMatrix.c: Duplicate the contents of the RHS before
459 :     Lapack call
460 : maechler 2043
461 : maechler 2036 2007-08-03 Martin Maechler <maechler@stat.math.ethz.ch>
462 :    
463 :     * R/Matrix.R (%*%, crossprod, tcrossprod): add method for
464 : maechler 2039 ("Matrix", "matrix") which is needed in some cases.
465 :     Ditto for solve().
466 : maechler 2036
467 :     * R/colSums.R (.as.dge.Fun): need ddenseMatrix methods to avoid
468 :     infinite recursion in dispatch for some cases.
469 :    
470 : bates 2041 2007-08-02 08:48 Martin Maechler <maechler@stat.math.ethz.ch>
471 : maechler 2036
472 : bates 2041 * [r4693] src/chm_common.c: R_cholmod_printf() instead of Rprintf() just
473 :     so pointers match
474 :    
475 : maechler 2024 2007-08-02 Martin Maechler <maechler@stat.math.ethz.ch>
476 :    
477 : maechler 2036 * DESCRIPTION (Date): set ready for release -- 0.999375-1
478 : maechler 2024
479 : bates 2020 2007-08-01 15:44 Douglas Bates <bates@stat.wisc.edu>
480 :    
481 :     * [r4686] inst/include/Matrix.h, inst/include/Matrix_stubs.c,
482 :     src/chm_common.c, src/chm_common.h: Change API for
483 :     numeric_as_chm_dense and N_AS_CHM_DN
484 : maechler 2024
485 : maechler 2018 2007-08-01 Martin Maechler <maechler@stat.math.ethz.ch>
486 :    
487 :     * src/dtrMatrix.c (dtrMatrix_matrix_mm): fix dimensionality check (!)
488 :     * tests/matprod.R: regr.test for it
489 :    
490 : maechler 2011 2007-07-20 Martin Maechler <maechler@stat.math.ethz.ch>
491 :    
492 :     * R/dMatrix.R: fix from Brian for Math2(., digits = "missing")
493 :     * tests/group-methods.R: and regression-test it
494 :    
495 : bates 2008 2007-07-19 19:45 Douglas Bates <bates@stat.wisc.edu>
496 :    
497 :     * [r4642] inst/include/Matrix.h, inst/include/Matrix_stubs.c,
498 :     inst/include/cholmod.h, src/chm_common.c, src/init.c: Export
499 :     triplet_to_sparse, documentation, use typedefs
500 : maechler 2011
501 : maechler 2005 2007-07-18 Martin Maechler <maechler@stat.math.ethz.ch>
502 :    
503 :     * man/dpoMatrix-class.Rd: added 'corMatrix' example
504 :    
505 :     * src/dsyMatrix.[ch] (dsyMatrix_as_matrix): new 'keep_dimnames' arg
506 :     * src/dtrMatrix.[ch] (dtrMatrix_as_matrix): ditto
507 :     * src/init.c, R/dsyMatrix.R, R/dtrMatrix.R, R/lgTMatrix.R: ditto
508 :    
509 :     * R/lsparseMatrix.R: bug fix in "all" method
510 :     * R/Ops.R (.do.Logic.lsparse): "|" bug in borderline case
511 :    
512 :     * R/dsyMatrix.R (coerce->dsTMatrix): (i,j) slots should *not* have names
513 :     * R/ngTMatrix.R (coerce->ngTMatrix): ditto;
514 :     + matrix |-> nMatrix coercion
515 :     * R/pMatrix.R: + setAs() to dMatrix and from nMatrix
516 :     * man/pMatrix-class.Rd: ditto
517 :    
518 :     * R/Matrix.R (Summary): method for non-dMatrix
519 :    
520 :     * tests/Class+Meth.R (extraValid): new check about "dirty" slots
521 :     * tests/Class+Meth.R (tstMatrixClass): test norm(.);
522 :     test all Summary methods.
523 :    
524 :     2007-07-16 Martin Maechler <maechler@stat.math.ethz.ch>
525 :    
526 :     * R/dgeMatrix.R (norm, rcond): methods for 'matrix'
527 :    
528 :     2007-07-14 Martin Maechler <maechler@stat.math.ethz.ch>
529 :    
530 :     * R/sparseMatrix.R (norm): simple methods for sparseMatrix
531 :    
532 :     * R/pMatrix.R (t?crossprod): methods for pMatrix
533 :    
534 : bates 1987 2007-07-10 Douglas Bates <bates@stat.wisc.edu>
535 :    
536 :     * src/dgeMatrix.c (dgeMatrix_colsums): Get the logic straight.
537 :    
538 : bates 1975 2007-07-09 20:45 Douglas Bates <bates@stat.wisc.edu>
539 :    
540 :     * [r4579] src/dgeMatrix.c: Untangle horrible code in dgeMatrix_colsums
541 : maechler 2005 trying to fix a subtle bug - which has been somewhere else.
542 : bates 1975
543 :     2007-07-09 19:43 Martin Maechler <maechler@stat.math.ethz.ch>
544 :    
545 :     * [r4578] src/dgeMatrix.c: "cleaned" dgeMatrix_colsums() - but did not
546 :     solve the bug
547 :    
548 : maechler 1968 2007-07-08 Martin Maechler <maechler@stat.math.ethz.ch>
549 : bates 1964
550 : maechler 1968 * src/dgCMatrix.c (compressed_to_TMatrix):
551 :    
552 :     2007-07-07 Martin Maechler <maechler@stat.math.ethz.ch>
553 :    
554 :     * src/Csparse.c (Rsparse_validate): new, to have some validity
555 :     checking for RsparseMatrix
556 :     * src/dgCMatrix.c (xRMatrix_validate): ditto
557 :     * src/dtCMatrix.c (tRMatrix_validate): ditto
558 :    
559 :     2007-07-07 Douglas Bates <bates@stat.wisc.edu>
560 :    
561 : bates 1964 * [r4567] R/AllClass.R: Slots already in RsparseMatrix were redefined in
562 :     lgRMatrix
563 :     * [r4568] DESCRIPTION: Prepare for bug-fix release
564 : bates 1966 * [r4570] src/CHOLMOD/Check/cholmod_write.c: Include cholmod_matrixops.h
565 :     for declaration of cholmod_symmetry
566 : maechler 1968
567 : maechler 1961 2007-07-06 Martin Maechler <maechler@stat.math.ethz.ch>
568 :    
569 :     * DESCRIPTION (Version): 0.999375 merged into the trunk; ready for
570 :     release.
571 :    
572 : maechler 1960 2007-07-06 14:11 Douglas Bates <bates@stat.wisc.edu>
573 :    
574 :     * [r4559] src/iohb.c, src/iohb.h: Remove Harwell-Boeing input/output
575 :     functions - no longer used
576 :     * [r4560] src/HBMM.c, src/Mutils.c, src/dgTMatrix.c, src/dgeMatrix.c,
577 :     src/dspMatrix.c, src/dsyMatrix.c, src/dtCMatrix.c,
578 :     src/factorizations.c, src/sparseQR.c: Replace most calls to Calloc by
579 :     Alloca
580 :    
581 :     2007-07-06 13:14 Martin Maechler <maechler@stat.math.ethz.ch>
582 :    
583 :     * [r4558] inst/doc/Comparisons.Rnw, src/CHMfactor.c, src/Csparse.c,
584 :     src/Tsparse.c, src/chm_common.c, src/chm_common.h, src/dense.c,
585 :     src/dgCMatrix.c, src/dsCMatrix.c, src/dtTMatrix.c, src/sparseQR.c,
586 :     src/t_gCMatrix_colSums.c: more R_CheckStack()s
587 :    
588 :     2007-07-05 18:12 Douglas Bates <bates@stat.wisc.edu>
589 :    
590 :     * [r4550] inst/include/Matrix.h: Add the macro N_AS_CHM_DN to "alloca"
591 :     the required amount of memory then call M_numeric_as_chm_dense.
592 :     * [r4556] src/Mutils.h, src/dgCMatrix.c: Define and use the Alloca macro
593 :     (like Calloc but calling alloca)
594 :    
595 : maechler 1947 2007-07-05 Martin Maechler <maechler@stat.math.ethz.ch>
596 :    
597 :     * R/sparseMatrix.R (printSpMatrix): renamed from prSpMatrix()
598 :     and extended with more sophisticated 'col.names' option.
599 :     * NAMESPACE: export printSparseMatrix()
600 :     * man/printSpMatrix.Rd: document, incl. examples
601 :    
602 : maechler 1960 2007-07-04 16:21 Douglas Bates <bates@stat.wisc.edu>
603 :    
604 :     * [r4543] src/cs_utils.c, src/cs_utils.h, src/dgCMatrix.c,
605 :     src/dtCMatrix.c, src/sparseQR.c: CSP typedef for *cs and macro
606 :     AS_CSP. API change - pass the empty structure to Matrix_as_cs.
607 :    
608 : maechler 1945 2007-07-04 Martin Maechler <maechler@stat.math.ethz.ch>
609 :    
610 :     * DESCRIPTION (Version): 0.99875-4
611 :    
612 :     * tests/Class+Meth.R (tstMatrixClass): add dimnames, and hence test
613 :     some dimnames perservation.
614 :    
615 :     * R/dsTMatrix.R (t-method): keep dimnames
616 :     * R/dtTMatrix.R: ditto
617 :    
618 :     * R/sparseMatrix.R (prSpMatrix): print colnames when non-trivial
619 :     and ncol(.) < 10
620 :    
621 :     * src/cs_utils.c: drop check_class() and use Matrix_check_class()
622 :     from Mutils.h
623 :    
624 :     * src/lgCMatrix.c ([ln]csc_to_matrix): no longer lose dimnames,
625 :     e.g. in as(<ngCMatrix>, "matrix")
626 :    
627 : maechler 1960 2007-07-01 13:27 Douglas Bates <bates@stat.wisc.edu>
628 :    
629 :     * [r4529] .: Create a branch for the API changes from the 0.99875
630 :     series to the 0.999375 series
631 :     * [r4530] DESCRIPTION, inst/include/Matrix.h,
632 :     inst/include/Matrix_stubs.c, src/CHMfactor.c, src/Csparse.c,
633 :     src/Mutils.h, src/Tsparse.c, src/chm_common.c, src/chm_common.h,
634 :     src/dense.c, src/dgCMatrix.c, src/dsCMatrix.c, src/dtTMatrix.c,
635 :     src/t_gCMatrix_colSums.c: API change - pass the empty structure to the
636 :     as_cholmod_x functions
637 :    
638 :     2007-06-30 09:05 Martin Maechler <maechler@stat.math.ethz.ch>
639 :    
640 :     * [r4527] trunk/Matrix/DESCRIPTION, trunk/Matrix/NAMESPACE,
641 :     trunk/Matrix/inst/doc/Comparisons.Rnw: add session- and hardware-info
642 :     to Comparisons
643 :    
644 :     >>>>>>> .merge-right.r4561
645 : maechler 1932 2007-06-29 Martin Maechler <maechler@stat.math.ethz.ch>
646 :    
647 :     * DESCRIPTION (Version): 0.99875-3 ready to be released.
648 :    
649 :     * R/sparseMatrix.R (spMatrix): make spMatrix(3,4) working
650 :    
651 :     * R/AllGeneric.R: set "Math" (and "Math2") group generics in a way
652 :     that should also work in a future version of R.
653 :    
654 : maechler 1922 2007-06-21 Martin Maechler <maechler@stat.math.ethz.ch>
655 :    
656 :     * NAMESPACE, R/AllClass.R: "xsparseVector" class union.
657 :    
658 :     * R/sparseVector.R: more *sparseVector coercions, notably for
659 :     non - double ones.
660 :    
661 : maechler 1911 2007-06-19 Martin Maechler <maechler@stat.math.ethz.ch>
662 :    
663 :     * R/colSums.R: new file for all (col|row)(Sums|Means) methods,
664 :     notably the new ones building on the new .Call(.)s:
665 :    
666 :     * src/dgCMatrix.c (DEF_gCMatrix_COLSUMS): use to define
667 :     all 4 of [dlin]gCMatrix_colSums().
668 :    
669 : bates 1909 2007-06-18 16:12 Douglas Bates <bates@stat.wisc.edu>
670 :    
671 :     * [r4472] src/Syms.h, src/init.c: Added Matrix_lengthSym
672 :     * [r4473] src/dgCMatrix.c: Modified dgCMatrix_colSums for sparseVector
673 :     result
674 : maechler 1911
675 : maechler 1903 2007-06-16 Martin Maechler <maechler@stat.math.ethz.ch>
676 :    
677 : maechler 1904 * R/kronecker.R: fix typo (could lead to inf.recursion)
678 :     * test/simple.R: testing that
679 :    
680 : maechler 1903 * R/sparseMatrix.R (prSpMatrix): change to be used as print()
681 : maechler 1922 method as well (which can have arguments, show() can't).
682 : maechler 1903
683 : bates 1902 2007-06-16 15:52 Douglas Bates <bates@stat.wisc.edu>
684 :    
685 :     * [r4466] R/dgCMatrix.R, src/dgCMatrix.c, src/dgCMatrix.h, src/init.c:
686 :     added dgCMatrix_colSums for [col,row][Sums,Means]
687 :    
688 : bates 1899 2007-06-15 23:15 Douglas Bates <bates@stat.wisc.edu>
689 : bates 1897
690 :     * [r4460] R/sparseMatrix.R, man/dgCMatrix-class.Rd, src/dgCMatrix.c,
691 :     src/dgCMatrix.h, src/init.c: added lm.fit.sparse (unexported),
692 :     coercion of "factor" to "dgCMatrix" and dgCMatrix_cholsol
693 :     * [r4461] R/AllClass.R, man/sparseMatrix-class.Rd: draft "indicators"
694 :     class
695 : bates 1899 * [r4463] R/sparseMatrix.R, man/dgCMatrix-class.Rd,
696 :     man/sparseMatrix-class.Rd: Don't need an "indicators" class - use the
697 :     row names to store the levels - duh! Added an example.
698 : maechler 1903
699 : maechler 1893 2007-06-14 Martin Maechler <maechler@stat.math.ethz.ch>
700 :    
701 :     * src/Csparse.c (Csparse_validate): check for *repeated* entries
702 :     thanks to example from Christian Buchta; with a test here:
703 :     * tests/simple.R:
704 :    
705 : maechler 1886 2007-06-07 Martin Maechler <maechler@stat.math.ethz.ch>
706 :    
707 :     * R/Auxiliaries.R (callGeneric): another fix, needed for some cases
708 :     of colSums(*, sparseResult = TRUE)
709 :    
710 : maechler 1883 2007-06-06 Martin Maechler <maechler@stat.math.ethz.ch>
711 :    
712 :     * R/lsparseMatrix.R, R/ldenseMatrix.R (all, any): change default to
713 :     'na.rm = FALSE' as "everywhere" else in R.
714 :    
715 : bates 1877 2007-06-05 Douglas Bates <bates@stat.wisc.edu>
716 :    
717 : bates 1878 * [r4421] src/CSparse_install.sh: Modify for new organization of
718 : maechler 1883 CSparse package
719 : bates 1877 * [r4425] src/UFsparse_download.sh: Update to version 3.0.0 of
720 :     SuiteSparse
721 :     * [r4426] src/Makefile: add ./UFconfig to the include path for
722 :     compilation
723 : maechler 1883 * [r4427] src/cs.[ch]: update to CSparse version 2.2.0
724 :     * [r4428] inst/doc/UFsparse/* src/{AMD,CHOLMOD,COLAMD}/*
725 :     src/UFconfig/UFconfig.h: Update to version 3.0.0 of SuiteSparse
726 :    
727 : maechler 1870 2007-06-05 Martin Maechler <maechler@stat.math.ethz.ch>
728 :    
729 :     * R/Auxiliaries.R (emptyColnames): + argument msg.if.not.empty, used in
730 :     * R/sparseMatrix.R (prSpMatrix): now gives a message about
731 :     suppressed column names.
732 :    
733 : bates 1868 2007-06-04 17:13 Douglas Bates <bates@stat.wisc.edu>
734 :    
735 :     * [r4418] src/Csparse.c, src/HBMM.c, src/Mutils.c, src/Mutils.h,
736 :     src/Tsparse.c, src/chm_common.c, src/chm_common.h, src/dgCMatrix.c,
737 :     src/dgeMatrix.c, src/dpoMatrix.c, src/dpoMatrix.h, src/dppMatrix.c,
738 :     src/dppMatrix.h, src/dsCMatrix.c, src/dspMatrix.c, src/dspMatrix.h,
739 :     src/dsyMatrix.c, src/dsyMatrix.h, src/dtpMatrix.c, src/dtrMatrix.c:
740 :     Remove warnings after change to const char* CHAR
741 :    
742 :     2007-06-04 17:11 Douglas Bates <bates@stat.wisc.edu>
743 :    
744 :     * [r4417] inst/include/Matrix_stubs.c, inst/include/cholmod.h: Corrected
745 :     type of M_cholmod_ssmult
746 :    
747 : bates 1863 2007-06-03 14:42 Douglas Bates <bates@stat.wisc.edu>
748 :    
749 :     * [r4412] inst/include/Matrix_stubs.c, inst/include/cholmod.h,
750 :     src/init.c: Yet another cholmod export - cholmod_ssmult
751 :    
752 : maechler 1855 2007-05-23 Martin Maechler <maechler@stat.math.ethz.ch>
753 :    
754 :     * NAMESPACE: exported drop0(), since
755 :     * man/drop0.Rd: I have seen several cases, I really wanted to use
756 :     it, so our users may want too.
757 :    
758 :     2007-05-22 Martin Maechler <maechler@stat.math.ethz.ch>
759 :    
760 :     * man/colSums.Rd: separately document colSums() etc, since these
761 :     have the extra argument 'sparseResult'.
762 :    
763 : maechler 1852 2007-05-21 Martin Maechler <maechler@stat.math.ethz.ch>
764 :    
765 :     * R/sparseMatrix.R (spMatrix): utility (T)sparse Matrix constructor;
766 :     * man/spMatrix.Rd: docu., including examples
767 :    
768 :     * R/Auxiliaries.R (sp.colMeans): etc, using a patched callGeneric(),
769 :     in order to make colMeans() etc fast *and* correct.
770 :     * R/sparseVector.R (replSPvec): "[<-" functionality for
771 :     sparseVectors; tested in
772 :     * tests/simple.R:
773 :    
774 :     2007-05-19 Martin Maechler <maechler@stat.math.ethz.ch>
775 :    
776 :     * R/sparseMatrix.R (print.sparseSummary): and summary() method for
777 :     (very) sparse Matrices; output similar to Matlab's print().
778 :    
779 : bates 1847 2007-05-17 Douglas Bates <bates@stat.wisc.edu>
780 :    
781 :     * src/HBMM.c (Matrix_writeMatrixMarket): Write 1-based, not
782 :     0-based, indices (Jose Quesada <quesada@gmail.com>).
783 :    
784 : bates 1844 2007-05-16 Douglas Bates <bates@stat.wisc.edu>
785 :    
786 :     * R/CHMfactor.R: Added solve methods for a CHMfactor object.
787 :    
788 : maechler 1845 2007-05-16 Martin Maechler <maechler@stat.math.ethz.ch>
789 :    
790 :     * R/Auxiliaries.R (sparsapply): new utility, much faster than
791 :     tapply1() for large sparse matrices.
792 :    
793 :     2007-05-15 Martin Maechler <maechler@stat.math.ethz.ch>
794 :    
795 :     * R/Matrix.R (dim<-): reshape now via sparseVector.
796 :    
797 :     * R/sparseVector.R: methods and function for
798 :     * R/AllClass.R: new "sparseVector" class and daughters.
799 :     * NAMESPACE: export new classes
800 :    
801 : maechler 1837 2007-05-14 Martin Maechler <maechler@stat.math.ethz.ch>
802 :    
803 :     * DESCRIPTION (Version): 0.99875-1
804 :     * src/Makefile.win: also remove Lapack code from here (cf. 04-25).
805 :    
806 : maechler 1834 2007-05-11 Martin Maechler <maechler@stat.math.ethz.ch>
807 :    
808 :     * R/Tsparse.R ([, Tsparse): fix last case: *duplicated*, symmetric
809 :     indexing
810 :     * tests/indexing.R: test set for that.
811 :    
812 : maechler 1833 2007-05-08 Martin Maechler <maechler@stat.math.ethz.ch>
813 :    
814 :     * R/Tsparse.R (replTmat): fix the case of *duplicated* index
815 :     entries.
816 :     * tests/indexing.R(out): add regression test for it
817 :    
818 :     2007-04-30 Martin Maechler <maechler@stat.math.ethz.ch>
819 :    
820 :     * R/(l(dense|sparse))?Matrix.R (!): use 'x', not 'e1' as argument
821 :     name for "!" method definitions.
822 :    
823 : maechler 1829 2007-04-26 Martin Maechler <maechler@stat.math.ethz.ch>
824 :    
825 :     * R/Tsparse.R (intI): new utility, used for "[" :
826 :     Cleanup up there, and fixes for duplicated indices - more TODO!
827 :    
828 :     * tests/indexing.R(out): more tests
829 :    
830 : bates 1827 2007-04-25 Douglas Bates <bates@stat.wisc.edu>
831 :    
832 :     * DESCRIPTION,src/Makefile: require R>= 2.5.0 and remove Lapack
833 :     code that is now part of the R Lapack library.
834 : maechler 1829
835 : bates 1827 * src/init.c,inst/include/{Matrix_stubs.c,cholmod.h}:export
836 :     cholmod_factorize_p (used in lme4 for GLMMs and NLMMs).
837 :    
838 : maechler 1829 2007-04-21 Martin Maechler <maechler@stat.math.ethz.ch>
839 :    
840 :     * R/Matrix.R (image): method for all Matrices, not just sparse ones.
841 :    
842 :     2007-04-17 Martin Maechler <maechler@stat.math.ethz.ch>
843 :    
844 :     * R/Auxiliaries.R (tapply1): unname(.) -> colSums() etc don't end
845 :     up with extraneous names '0'...'<n-1>'
846 :    
847 : maechler 1825 2007-04-12 Martin Maechler <maechler@stat.math.ethz.ch>
848 :    
849 :     * R/dgTMatrix.R (mat2dgT): care about NAs
850 :    
851 :     2007-04-11 Martin Maechler <maechler@stat.math.ethz.ch>
852 :    
853 :     * R/kronecker.R: triangularity preserving methods
854 :    
855 : maechler 1803 2007-03-27 Martin Maechler <maechler@stat.math.ethz.ch>
856 :    
857 :     * R/kronecker.R: new file collecting kronecker() methods in one
858 :     place. Goal: become much faster!
859 :    
860 : maechler 1799 2007-03-23 Martin Maechler <maechler@stat.math.ethz.ch>
861 :    
862 :     * src/dtCMatrix.c (dtCMatrix_solve): use the new code from Kasper
863 :     Kristensen based cs_spsolve() instead of _lsolve & _usolve which
864 :     can be much faster.
865 :    
866 :     * tests/matprod.R: add regression tests for these (upper & lower).
867 :    
868 :     2007-03-19 Martin Maechler <maechler@stat.math.ethz.ch>
869 :    
870 :     * R/Matrix.R (diff): method for our Matrices.
871 :    
872 :     * R/sparseMatrix.R (isDiagonal): check dim()!
873 :    
874 :     2007-03-17 Martin Maechler <maechler@stat.math.ethz.ch>
875 :    
876 :     * R/Matrix.R (dim<-): new method for "reshape()" built on a
877 :     proposal from Tamas Papp.
878 :    
879 :     2007-03-16 Martin Maechler <maechler@stat.math.ethz.ch>
880 :    
881 :     * R/AllGeneric.R: remove all if(!isGeneric(.)) clauses
882 :    
883 :     * R/zzz.R (.onLoad, .onUnload): do *not* leave bind_activation(TRUE);
884 : maechler 1803 rather define and export cBind() and rBind() only.
885 :     --> useRs *must* change code that used to have cbind()/rbind() !!
886 : maechler 1799
887 : maechler 1803 * R/bind.R: change tests from cbind() to cBind() and similarly to rBind()
888 :     * R/bind.Rout.save: ditto
889 : maechler 1799
890 : bates 1787 2007-02-16 Douglas Bates <bates@r-project.org>
891 :    
892 :     * DESCRIPTION (Date, Version): 0.9975-11 with new date
893 :     * src/dgCMatrix.c (R_to_CMatrix, compressed_to_TMatrix): remove
894 :     const modifier on declaration of the array 'valid'
895 :    
896 : bates 1786 2007-02-12 Douglas Bates <bates@stat.wisc.edu>
897 :    
898 :     * R/CHMfactor.R: Add image method (coercion to sparseMatrix).
899 :    
900 : maechler 1765 2007-02-05 Martin Maechler <maechler@stat.math.ethz.ch>
901 :    
902 : maechler 1768 * DESCRIPTION (Date, Version): 0.9975-10 with new date.
903 :    
904 : maechler 1767 * R/Ops.R (Arith): make sure Csparse o Csparse also works for e.g. ntCMatrix
905 :     * tests/simple.R: test the above and some of these coercions:
906 :    
907 :     * R/nsparseMatrix.R: coercing "Csparse" to "lsparseMatrix";
908 :     be careful to avoid infinite recursion, using new coercions in
909 :     * R/ngCMatrix.R and nsC... and ntC...
910 :     * R/lsparseMatrix.R: ditto
911 :    
912 : maechler 1765 * R/SparseM-conv.R: more conversion, notably for triplet matrices.
913 :    
914 : maechler 1767 * src/dgCMatrix.c (R_to_C_Matrix): port Doug's fix and
915 :     * R/Rsparse.R: reactivate .Call()s
916 : maechler 1765
917 : maechler 1767 * tests/Class+Meth.R: a bit more on actual classes
918 :    
919 :     2007-02-04 Douglas Bates <bates@stat.wisc.edu>
920 :    
921 :     * src/dgCMatrix.c (compressed_to_TMatrix): fix memory bug using strdup()
922 :    
923 : maechler 1760 2007-02-03 Martin Maechler <maechler@stat.math.ethz.ch>
924 : maechler 1758
925 :     * DESCRIPTION (Version): 0.9975-10 to upload
926 :    
927 : maechler 1760 * tests/Class+Meth.R (tstMatrixClass): require coercions to
928 :     specific classes less unconditionally.
929 :    
930 :     * R/Auxiliaries.R: get rid of as_Tsparse() and as_Rsparse()
931 :    
932 :     * R/Tsparse.R (triu): etc, use as(*, "TsparseMatrix") instead of as_Tsparse()
933 :    
934 :     * R/Rsparse.R (.R.2.T): R-level workaround using compressed_to_TMatrix.
935 : maechler 1758 * R/Rsparse.R (.R.2.C): R-level workaround since C-level
936 :     R_to_CMatrix segfaults on one platform.
937 : maechler 1760 Eliminate most coercion method to *specific* classes, and replace
938 :     with virtual classes coercions.
939 : maechler 1758
940 : maechler 1760
941 : maechler 1758 2007-02-01 Martin Maechler <maechler@stat.math.ethz.ch>
942 :    
943 :     * src/init.c: export the CHM...._validate() placeholders, since
944 :     they *are* called.
945 :    
946 : maechler 1760 * tests/Class+Meth.R (classCanCoerce): and starting to test
947 : maechler 1758 all as(<from>, <to>)
948 :    
949 : maechler 1751 2007-01-30 Martin Maechler <maechler@stat.math.ethz.ch>
950 :    
951 :     * R/Tsparse.R ([): more care when subsetting triangular Tsparse
952 :     * tests/indexing.R: tested now
953 :     * tests/indexing.Rout.save: updated
954 :    
955 :     * src/Csparse.c (Csparse_to_dense): use Rkind = -1 for PATTERN to
956 :     * src/chm_common.c (chm_dense_to_SEXP): return "ngeMatrix" when
957 :     appropriate.
958 :    
959 :     * NAMESPACE: export a trivial
960 :     * R/Matrix.R: drop() Matrix-method
961 :    
962 :     * R/AllClass.R: moved all prototypes to virtual super classes.
963 :    
964 :     * R/Rsparse.R: many more coercions to have less exceptions in
965 :     * tests/Class+Meth.R:
966 :    
967 :     * R/Ops.R (Compare): tweak for case with NA
968 :     * tests/simpl.R: hence another 'FIXME' eliminated
969 :    
970 : maechler 1747 2007-01-29 Martin Maechler <maechler@stat.math.ethz.ch>
971 :    
972 : maechler 1748 * R/diagMatrix.R (solve): the obvious methods for diagonalMatrix
973 :     objects.
974 :    
975 : maechler 1747 * tests/Class+Meth.R (tstMatrixClass): now testing diag(), nnzero(),
976 :     and more of "!", "&", "|", all, any; coercions
977 :    
978 :     * R/Rsparse.R: many coercions (which enable quite a few other
979 :     methods), thanks to enhancements in
980 :     * src/dgCMatrix.c (R_to_CMatrix): new, and
981 :     * src/dgCMatrix.c (compressed_to_TMatrix): now for (d,l,n) ,
982 :     symmetric & triangular and ..RMatrix objects.
983 :    
984 :     * src/TMatrix_as.c (Matrix_T_as_DENSE,Matrix_T_as_GENERAL):
985 :     renamed file from src/dsTMatrix.c;
986 :     now dealing with symmetric and triangular Tsparse coercions, both
987 :     to dense and general.
988 :    
989 :     2007-01-27 Martin Maechler <maechler@stat.math.ethz.ch>
990 :    
991 :     * src/dsTMatrix.c: has now "l" and "n" methods besides the "d" ones.
992 :    
993 :     * R/Ops.R (Arith): <dgCMatrix> o <numeric> now remains sparse
994 :     where sensible when the <numeric> is of length > 1.
995 :    
996 :     2007-01-26 Martin Maechler <maechler@stat.math.ethz.ch>
997 :    
998 :     * R/Matrix.R ([<-): for M[] <- value: fix length
999 :    
1000 :     2007-01-25 Martin Maechler <maechler@stat.math.ethz.ch>
1001 :    
1002 :     * R/Auxiliaries.R (n2l_Matrix): new, to be used in
1003 :     * R/ndenseMatrix.R: new coercions n* -> l*
1004 :    
1005 : maechler 1738 2007-01-22 Martin Maechler <maechler@stat.math.ethz.ch>
1006 :    
1007 :     * R/triangularMatrix.R: new file; simple triu() and tril() methods.
1008 :    
1009 :     * R/Ops.R ("Logic"): and other "Ops", many updates
1010 :    
1011 :     2007-01-18 Martin Maechler <maechler@stat.math.ethz.ch>
1012 :    
1013 :     * src/Mutils.h (SET_DimNames): new utility
1014 :    
1015 :     * R/Auxiliaries.R (nnzero): improved and now exported via
1016 :    
1017 :     * NAMESPACE: + nnzero(); length() == prod(dim(.)) method for all "Matrix" objects
1018 :    
1019 : maechler 1725 2007-01-17 Martin Maechler <maechler@stat.math.ethz.ch>
1020 :    
1021 :     * R/diagMatrix.R (!): fix typo.
1022 :    
1023 :     2007-01-16 Martin Maechler <maechler@stat.math.ethz.ch>
1024 :    
1025 :     * R/Auxiliaries.R (as_Csparse): and quite a few others:
1026 :     allow to pass class definition --> speedup
1027 :     * R/sparseMatrix.R: apply the above
1028 :    
1029 :     * R/Csparse.R: coercion Csparse* to dense* now preserves shape properties.
1030 :    
1031 :     * src/Mutils.h (mMatrix_as_geMatrix): new, based on
1032 :     * src/Mutils.c (dup_mMatrix_as_geMatrix): new; generalization of
1033 :     old dup_mMatrix_as_dgeMatrix), eliminating a long-standing "FIXME".
1034 :    
1035 :     * src/dense.c (dense_to_Csparse): use new mMatrix_as_geMatrix()
1036 :    
1037 :     * R/denseMatrix.R (.dense2C): based on dense_to_Csparse: name it,
1038 :     and use it for "sparse*" as well, since it's faster than the
1039 :     as_Csparse(.) way.
1040 :    
1041 :     2007-01-15 Martin Maechler <maechler@stat.math.ethz.ch>
1042 :    
1043 :     * R/Ops.R ("Logic"): more methods, notably an <lgC> o <lgC> one.
1044 :    
1045 : maechler 1724 2007-01-12 Martin Maechler <maechler@stat.math.ethz.ch>
1046 :    
1047 :     * R/Tsparse.R (.TM.repl.i.2col): new internal function to be used
1048 :     as method for M[ ij ] <- v
1049 :     * R/Csparse.R:: go via Tsparse for "M[ij] <- v"
1050 :    
1051 :     * R/Ops.R: "Compare" for (C|R)sparse: need pointer slot for all
1052 :     FALSE answer
1053 :    
1054 :     * R/Csparse.R (replCmat): fix the "all non-zero" case with reordering
1055 :     * tests/indexing.R: test it, and some of the above
1056 :    
1057 :     2007-01-05 Martin Maechler <maechler@stat.math.ethz.ch>
1058 :    
1059 :     * R/Auxiliaries.R (is_duplicatedT): new utility
1060 :    
1061 : bates 1716 2007-01-05 Douglas Bates <bates@stat.wisc.edu>
1062 :    
1063 :     * src/init.c (R_init_Matrix): export cholmod_scale
1064 :    
1065 : maechler 1724 2006-12-30 Martin Maechler <maechler@stat.math.ethz.ch>
1066 :    
1067 :     * R/zzz.R (tmp): for R >= 2.5.0, extend formals of our
1068 :     base::as.matrix to (x, ...)
1069 :    
1070 : maechler 1714 2006-12-28 Martin Maechler <maechler@stat.math.ethz.ch>
1071 :    
1072 :     * R/Ops.R ("Arith" etc): move almost all "Ops" methods to new R
1073 :     file; start using "Logic", hence
1074 :    
1075 :     * DESCRIPTION (Depends): R >= 2.4.1 (since we want "Logic")
1076 :     * NAMESPACE: import and export "Logic"
1077 :    
1078 :     2006-12-27 Martin Maechler <maechler@stat.math.ethz.ch>
1079 :    
1080 :     * src/zpotfr.f and dependencies: use LAPACK 3.1 version
1081 :     only needed previously to R version 2.5.0.
1082 : maechler 1724
1083 : maechler 1710 2006-12-26 Martin Maechler <maechler@stat.math.ethz.ch>
1084 :    
1085 :     * DESCRIPTION (Date, Version): 0.9975-8, ready for release
1086 :    
1087 :     * R/Tsparse.R (replTmat): fix subassignment of triangular
1088 :     * R/Csparse.R (replCmat): ditto
1089 :     * tests/indexing.R: more tests, incl the above fix
1090 :    
1091 :     2006-12-23 Martin Maechler <maechler@stat.math.ethz.ch>
1092 :    
1093 :     * R/Auxiliaries.R (drop0): extend for non CSparse
1094 :     * R/Auxiliaries.R (diagU2N): should work for all sparseMatrix
1095 :    
1096 :     * src/Csparse.c (Csparse_to_Tsparse, Csparse_general_to_symmetric):
1097 :     use uplo correctly (!); other places: use uplo_P() macro
1098 :    
1099 :     * R/Csparse.R (replCmat): call diagU2N() when needed
1100 :     * R/Tsparse.R (replTmat): ditto
1101 :    
1102 :     * src/dtCMatrix.c (tCMatrix_validate): new
1103 :     * src/dtTMatrix.c (tTMatrix_validate): new, used in
1104 :     * R/AllClass.R: for validity of dtC, dsC, and dtT, dsT.
1105 :    
1106 :     * R/diagMatrix.R (replDiag): to use in [<-
1107 :    
1108 : maechler 1708 2006-12-22 Martin Maechler <maechler@stat.math.ethz.ch>
1109 :    
1110 :     * R/Auxiliaries.R (as_Csparse2, as_geSimpl): new functions;
1111 :     also more general diagU2N().
1112 :    
1113 :     2006-12-21 Martin Maechler <maechler@stat.math.ethz.ch>
1114 :    
1115 :     * R/bind2.R: new file for all cbind2(), rbind() methods moved here
1116 :     from R/<foo>Matrix.R files. Better diagonal & improved sparse methods.
1117 :    
1118 : maechler 1707 2006-12-20 Martin Maechler <maechler@stat.math.ethz.ch>
1119 :    
1120 :     * tests/bind.R: a few more cases
1121 :     * R/Auxiliaries.R (.M.kind): also work for atomic vectors
1122 :    
1123 :     * R/denseMatrix.R (cbind2/rbind2): moved here (and generalized) from
1124 :     * R/ddenseMatrix.R (cbind2/rbind2)
1125 :     * R/Tsparse.R (replTmat): final(?!) fix for "[<-" ..
1126 :     * tests/indexing.R
1127 :     * tests/indexing.Rout.save: updated
1128 :    
1129 :     2006-12-18 Martin Maechler <maechler@stat.math.ethz.ch>
1130 :    
1131 :     * R/Tsparse.R (replTmat): fixed a remaining "[<-" bug in
1132 :     * tests/indexing.R
1133 :    
1134 : maechler 1705 2006-12-15 Martin Maechler <maechler@stat.math.ethz.ch>
1135 :    
1136 :     * R/sparseMatrix.R (prSpMatrix): "." alignment much improved:
1137 :     align with proper position of "0", i.e., right for integers.
1138 :     argument 'align' by default is "fancy".
1139 :    
1140 :     2006-12-14 Martin Maechler <maechler@stat.math.ethz.ch>
1141 :    
1142 :     * R/sparseMatrix.R: delegate "Compare" to "Csparse.."
1143 :     * R/Csparse.R: and fix "Compare" for more cases.
1144 :     * tests/Class+Meth.R: test some of these (m == m, m != m)
1145 :    
1146 :     2006-12-13 Martin Maechler <maechler@stat.math.ethz.ch>
1147 :    
1148 :     * R/lsparseMatrix.R: all() and any() methods
1149 :     * R/ldenseMatrix.R: ditto
1150 :     * NAMESPACE, R/Matrix.R: ditto
1151 :    
1152 :     * man/all-methods.Rd: document them minimally
1153 :    
1154 :     * tests/simple.R: add a few examples for these
1155 :    
1156 : maechler 1696 2006-12-11 Martin Maechler <maechler@stat.math.ethz.ch>
1157 :    
1158 :     * R/Tsparse.R ([): fix long standing typo in symmetric case
1159 :     * man/dsCMatrix-class.Rd: add example exhibiting the above case
1160 :    
1161 : bates 1691 2006-12-10 Douglas Bates <bates@stat.wisc.edu>
1162 :    
1163 :     * src/CHMfactor.c (CHMfactor_to_sparse): change LDL factorization
1164 :     to LL before converting to a sparse matrix. (The LDL form can be
1165 :     converted to a sparse matrix but it is implicitly a unit
1166 :     triangular matrix and a diagonal matrix overwritten on the diagonal.)
1167 :    
1168 :     2006-12-09 Douglas Bates <bates@stat.wisc.edu>
1169 :    
1170 :     * src/chm_common.c (chm_factor_to_SEXP): allocate and fill the Dim slot.
1171 :    
1172 : bates 1688 2006-12-08 Douglas Bates <bates@stat.wisc.edu>
1173 :    
1174 :     * DESCRIPTION (Version): updated -> release 0.9975-7
1175 :     * src/{init.c,chm_common.c}, inst/include/*: export cholmod_analyze_p
1176 :    
1177 : maechler 1682 2006-11-30 Martin Maechler <maechler@stat.math.ethz.ch>
1178 :    
1179 :     * R/diagMatrix.R (%*%): write a direct [diag o Csparse] method
1180 :    
1181 : bates 1681 2006-11-29 Douglas Bates <bates@stat.wisc.edu>
1182 :    
1183 :     * src/dgeMatrix.c (dgeMatrix_solve): Check error code from dgetri.
1184 :     * tests/dg_Matrix.R: Add Barry Rowlingson's test of a matrix that
1185 :     is exactly singular.
1186 :    
1187 : maechler 1674 2006-11-07 Martin Maechler <maechler@stat.math.ethz.ch>
1188 :    
1189 :     * DESCRIPTION (Date): updated -> release 0.9975-6
1190 :    
1191 : maechler 1673 2006-11-06 Martin Maechler <maechler@stat.math.ethz.ch>
1192 :    
1193 :     * R/Csparse.R (replCmat): symmetric indexing of symmetric matrix
1194 :     now returns symmetric.
1195 :    
1196 :     * R/zzz.R ("diag<-"): replace "diag<-" in base for R <= 2.4.x
1197 :    
1198 :     * R/Matrix.R (.M.sub.i.2col): new, for M[ cbind(i,j) ] indexing.
1199 :     * R/Matrix.R (.M.repl.i.2col): new, for M[ cbind(i,j) ] <- value
1200 :    
1201 :     * R/Auxiliaries.R (.type.kind): added
1202 :    
1203 :     2006-11-04 Martin Maechler <maechler@stat.math.ethz.ch>
1204 :    
1205 :     * src/cs.[ch]: updated to CSparse Version 2.0.3 by simply
1206 :     running src/CSparse_install.sh
1207 :    
1208 :     * R/denseMatrix.R: "[": keep symmetric on symmetric indexing.
1209 :    
1210 : maechler 1665 2006-11-03 Martin Maechler <maechler@stat.math.ethz.ch>
1211 :    
1212 :     * src/dsCMatrix.c (dsCMatrix_Csparse_solve): new
1213 :     * R/dsCMatrix.R (solve): "fully-sparse" using the above.
1214 :    
1215 :     * R/AllClass.R: "pMatrix" now also inherits from "generalMatrix"
1216 :    
1217 :     * tests/Class+Meth.R (tstMatrixClass): now assure
1218 :     the (important in method programming) property :
1219 :    
1220 :     ###>> Every "Matrix" is either
1221 :     ###>> "general*", "symmetric*", "triangular*" or "diagonal*"
1222 :    
1223 :     (where "*" stands for "Matrix")
1224 :    
1225 :     * R/Auxiliaries.R (diagU2N): now .Call()s Csparse_diagU2N for <Csparse>
1226 :    
1227 :     * R/dMatrix.R (Compare(<dMatrix>,<dMatrix>): update and
1228 :     * tests/validObj.R: checks for "comparison"
1229 :    
1230 :     * R/sparseMatrix.R ([): improved indexing for sparse;
1231 :     trying to keep <symmetric>[ n, n] symmmetric
1232 :    
1233 :     * tests/indexing.R: indexing for logical sparse now ok
1234 :    
1235 :    
1236 : maechler 1660 2006-11-02 Martin Maechler <maechler@stat.math.ethz.ch>
1237 :    
1238 : maechler 1661 * src/Tsparse.c: use xTsparse_validate() , and hence remove
1239 :    
1240 :     * src/{ltC,lsC,lgT}Matrix.[ch]: removed
1241 :    
1242 :     2006-11-02 Martin Maechler <maechler@stat.math.ethz.ch>
1243 :    
1244 : maechler 1660 * R/AllClass.R (Matrix-class): check length of dimnames in validity.
1245 :    
1246 :     * tests/simple.R: validObject() checking the above.
1247 :    
1248 : maechler 1665 * src/dgCMatrix.c (xCMatrix_validate): new, small and simple,
1249 : maechler 1660 replacing both dgCMatrix_validate and lgCM*.
1250 :    
1251 :     * src/Csparse.c (Csparse_dense_prod, etc): do not lose dimnames;
1252 :     fix dimnames setting in other places.
1253 :     * src/chm_common.c (chm_dense_to_SEXP): now can pass dimnames
1254 :    
1255 : maechler 1659 2006-11-01 Martin Maechler <maechler@stat.math.ethz.ch>
1256 :    
1257 : maechler 1660 * R/Csparse.R,src/Csparse.c, etc: tcrossprod(<CsparseM>,<CsparseM>)
1258 :    
1259 :     * R/sparseMatrix.R (isSymmetric): drop 'factors' slot for
1260 :     symmetry test, via
1261 : maechler 1659 * R/Auxiliaries.R (.as.dgC.0.factors):
1262 :    
1263 : bates 1657 2006-11-01 Douglas Bates <bates@r-project.org>
1264 :    
1265 :     * R/Csparse.R,src/Csparse.c,tests/matprod.R,
1266 :     man/CsparseMatrix-class.Rd: crossprod(<CsparseMatrix>,
1267 :     <CsparseMatrix>) added
1268 :    
1269 : maechler 1655 2006-10-30 Martin Maechler <maechler@stat.math.ethz.ch>
1270 :    
1271 :     * tests/matprod.R: add a variation of Harri's example
1272 :    
1273 :     * R/dsparseMatrix.R: fix crossprod(<dsparse>, <dge>) to *not*
1274 :     recursive infinitely.
1275 :    
1276 :     * R/dgCMatrix.R: + solve(<sparse>, <sparse>)
1277 :    
1278 :     * tests/indexing.R: add test for the "<" bug fixed 10-27 in R/dMatrix.R
1279 :    
1280 :     2006-10-28 Martin Maechler <maechler@stat.math.ethz.ch>
1281 :    
1282 :     * tests/Class+Meth.R (tstMatrixClass): more: use non-trivial
1283 :     matrix if possible; test m+m == 2*m; now test dgRMatrix.
1284 :     * R/dgRMatrix.R (.to.dgR): a few more coercions, in order to
1285 :     satisfy the above test.
1286 :    
1287 : maechler 1654 2006-10-27 Martin Maechler <maechler@stat.math.ethz.ch>
1288 :    
1289 : maechler 1655 * R/Matrix.R (Ops): <Matrix> o <matrix> method added
1290 :    
1291 : maechler 1654 * R/dgCMatrix.R: solve(a, b="missing") based on
1292 :     * src/dgCMatrix.c (dgCMatrix_matrix_solve): extend to work with
1293 :     RHS = NULL.
1294 :    
1295 :     * R/diagMatrix.R (diagdiagprod): extend %*% etc to ldiMatrix;
1296 :     add more (needed) [t]crossprod() methods.
1297 :    
1298 :     * man/ddiMatrix-class.Rd: more info, notably on 'diag'
1299 :    
1300 :     * R/Auxiliaries.R (as_CspClass): cleanup
1301 :     (drop0): internal utility for "Csparse_drop(*, 0)"
1302 :     (.bail.out.2): encourage active feedback
1303 :    
1304 :     2006-10-26 Martin Maechler <maechler@stat.math.ethz.ch>
1305 :    
1306 :     * R/dMatrix.R(Compare): new(), then slots [no validity check]
1307 :    
1308 :     * src/Csparse.c (Csparse_validate): fixed (and more efficient in
1309 :     non-valid or 'sorted' case).
1310 :    
1311 :     * R/dsparseMatrix.R: add "chol" method.
1312 :     * R/ddenseMatrix.R: ditto
1313 :    
1314 :     * R/diagMatrix.R (Ops): group methods for <diagonal> o <sparse>
1315 :     * NAMESPACE (Ops)
1316 :     * R/diagMatrix.R (diag2T): simple utility used "higher level"
1317 :     coercion; deprecating direct lower level coercions.
1318 :    
1319 :     * R/*.R (seq): use seq_len() and seq_along() where possible.
1320 :    
1321 :    
1322 : maechler 1647 2006-10-23 Martin Maechler <maechler@stat.math.ethz.ch>
1323 :    
1324 :     * DESCRIPTION (Version): 0.9975-5 ready for release
1325 :    
1326 : bates 1646 2006-10-20 Douglas Bates <bates@stat.wisc.edu>
1327 :    
1328 :     * src/init.c (R_init_Matrix): export more cholmod CCallable functions.
1329 :    
1330 : maechler 1642 2006-10-20 Martin Maechler <maechler@stat.math.ethz.ch>
1331 :    
1332 :     * R/AllClass.R (corMatrix): add 'validity' check;
1333 :     comment out unused "LDL" class definition
1334 :     * NAMESPACE: mention, but do not export "LDL" class
1335 :     * R/corMatrix.R: new (simple), needed for R-devel with
1336 :     * tests/Class+Meth.R (tstMatrixClass): 1 exception for corMatrix
1337 :     coerce and t() exceptions for all 5 'Mat.MatFact' classes.
1338 :    
1339 : bates 1641 2006-10-19 Douglas Bates <bates@stat.wisc.edu>
1340 :    
1341 :     * src/chm_common.h: Add R_cholmod_start to initialize cholmod to
1342 :     use Rprintf and R's error handling.
1343 :    
1344 : maechler 1635 2006-10-17 Martin Maechler <maechler@stat.math.ethz.ch>
1345 :    
1346 :     * R/diagMatrix.R (%*%): rep(*, each = .) in Matrix %*% diagonal.
1347 :     * tests/matprod.R: add tests for the bug fixed.
1348 :    
1349 : bates 1624 2006-10-11 Douglas Bates <bates@stat.wisc.edu>
1350 :    
1351 :     * src/HBMM.[ch]: remove HarwellBoeing format for writing.
1352 :     * src/SOURCES_C.mkf (SOURCES_C): no longer compile iohb.c
1353 :    
1354 :     2006-10-06 Douglas Bates <bates@stat.wisc.edu>
1355 :    
1356 : bates 1629 * R/d[gs]CMatrix.R: deprecate the writeHB function. Use writeMM instead.
1357 : bates 1624
1358 : maechler 1618 2006-10-06 Martin Maechler <maechler@stat.math.ethz.ch>
1359 :    
1360 :     * DESCRIPTION (Version): 0.9975-3
1361 :    
1362 :     * R/diagMatrix.R (bdiag): new function constructing block diagonal
1363 :     (sparse) matrices.
1364 :     * man/bdiag.Rd: docu + examples
1365 :    
1366 : maechler 1619 * R/Csparse.R (replCmat): calling new Csparse_drop() now.
1367 :    
1368 : maechler 1618 * src/Csparse.c (Csparse_general_to_symmetric, Csparse_drop): new functions
1369 :     * R/lsCMatrix.R: three more coercions to lsC (thanks to the above)
1370 :    
1371 :     * R/diagMatrix.R (Diagonal): '[<-' method for diag.matrices such
1372 :     that result is sparse or diagonal (and not dense).
1373 :    
1374 :     * man/Subassign-methods.Rd: fix examples
1375 :    
1376 :     * R/Matrix.R (Matrix): Matrix(0, *) or Matrix(*, sparse=TRUE)
1377 :     should always return a sparse (and not sometimes a diagonal) matrix.
1378 :    
1379 : maechler 1615 2006-10-05 Martin Maechler <maechler@stat.math.ethz.ch>
1380 :    
1381 :     * R/Matrix.R ([<-): also for value "Matrix" or "matrix"
1382 :    
1383 : bates 1613 2006-10-04 Douglas Bates <bates@stat.wisc.edu>
1384 :    
1385 :     * DESCRIPTION (Version): 0.9975-2
1386 : maechler 1615
1387 : bates 1613 * inst/include/Matrix_stubs.c (M_cholmod_sparse_to_triplet): export more symbols
1388 :    
1389 : bates 1611 2006-10-02 Douglas Bates <bates@R-project.org>
1390 :    
1391 :     * tests/dg_Matrix.R: Simplify test taking into account new code.
1392 :    
1393 : maechler 1599 2006-09-29 Martin Maechler <maechler@stat.math.ethz.ch>
1394 :    
1395 : maechler 1600 * R/Csparse.R (replCmat): improve for missing i / j in non-simple cases
1396 :    
1397 : maechler 1599 * R/lsTMatrix.R: new files w/ missing methods
1398 :     * R/nsTMatrix.R: " 'for completeness'
1399 :    
1400 :     * tests/Class+Meth.R: a bit less 'not.ok.classes'
1401 :    
1402 :     * R/Tsparse.R (t): generalized "t" method from "dgT*" to "Tsparse*"
1403 :    
1404 :    
1405 : bates 1595 2006-09-28 Douglas Bates <bates@R-project.org>
1406 :    
1407 :     * src/dppMatrix.h: Ensure definition of dspMatrix_validate is
1408 :     included.
1409 :    
1410 :     * src/init.c, inst/include/{Matrix.h,Matrix_stubs.h,cholmod.h}:
1411 :     Export C-callable functions used in Zt_create in lme4.
1412 :    
1413 : maechler 1592 2006-09-28 Martin Maechler <maechler@stat.math.ethz.ch>
1414 :    
1415 :     * DESCRIPTION (Version): 0.9975-1
1416 :    
1417 :     * tests/simple.R: less checks fail; using NA, found that our
1418 :     kronecker() is not base-compatible with NA's.
1419 :    
1420 :     * R/dMatrix.R: "Compare" method now implemented for all cases
1421 :    
1422 :     * R/Auxiliaries.R (indTri): == which([lower/upper].tri( * )) new utility
1423 :    
1424 :     * man/dtpMatrix-class.Rd: mention length of 'x' slot
1425 :    
1426 :     * src/dtpMatrix.c (dtpMatrix_validate): fix check
1427 :     * src/dspMatrix.c (dspMatrix_validate): ditto
1428 :    
1429 :     * R/dtTMatrix.R (gt2tT): fix ("l" -> "n")
1430 :     including coercion to [nl]tTMatrix.
1431 :    
1432 :     * R/diagMatrix.R (show): print a header line as for other classes.
1433 :    
1434 :     2006-09-27 Martin Maechler <maechler@stat.math.ethz.ch>
1435 :    
1436 :     * src/Makefile.win (SUBDIRS): fix typo
1437 :    
1438 : maechler 1583 2006-09-19 Martin Maechler <maechler@stat.math.ethz.ch>
1439 :    
1440 :     * DESCRIPTION (Date): ready to release 0.9975-0 to CRAN
1441 :    
1442 : bates 1577 2006-09-18 Douglas Bates <bates@stat.wisc.edu>
1443 :    
1444 :     * R/[CT]sparse.R (crossprod and tcrossprod): Handle the cases for x
1445 :     symmetric and y missing in R code using %*% (cholmod_aat doesn't
1446 :     accept a symmetric matrix).
1447 :     * tests/group-methods.R: Uncomment test of crossprod applied to
1448 :     lsCMatrix objects.
1449 :    
1450 : maechler 1575 2006-09-18 Martin Maechler <maechler@stat.math.ethz.ch>
1451 :    
1452 :     * R/AllClass.R (symmetricMatrix): add validity method (available
1453 :     in C for a long time). Many "n..Matrix": drop (wrong) validity arg.
1454 :    
1455 :     * src/lgCMatrix.c (lgCMatrix_validate): check 'x' slot (!)
1456 :    
1457 :     * tests/indexing.Rout.save:
1458 :     * tests/indexing.R: additions, mainly for 'lsparse'
1459 :    
1460 :     * R/diagMatrix.R (Diagonal) & coercion to lgTMatrix: fixes for NA
1461 :     case.
1462 :    
1463 :     * R/Auxiliaries.R (nz.NA): new utility now used in nnzero()
1464 :    
1465 : maechler 1571 2006-09-16 Martin Maechler <maechler@stat.math.ethz.ch>
1466 :    
1467 : maechler 1572 * R/sparseMatrix.R (prSpMatrix): print logical NAs "visibly"
1468 :     as 'N' (1-letter - Ok?)
1469 :    
1470 : maechler 1571 * tests/group-methods.R: add test for logical + NAs
1471 :    
1472 :     * R/dMatrix.R ("Compare"): fix to work with NA's
1473 :    
1474 :     * R/AllClass.R: "Cholesky" etc now inherit from MatrixFactorization.
1475 :    
1476 :     * src/lgCMatrix.c (ncsc_to_matrix): renamed from lcsc_to_matrix()
1477 :     which is implemented.
1478 :    
1479 : maechler 1565 2006-09-15 Martin Maechler <maechler@stat.math.ethz.ch>
1480 :    
1481 : maechler 1571 * src/chm_common.c: coerce logical <-> double instead of
1482 :     typecasting; needed for "l" matrix handling in cholmod.
1483 : maechler 1565
1484 : maechler 1571 * tests/other-pkgs.R (graph): small extension in "graph" checks.
1485 :    
1486 : maechler 1565 * R/sparseMatrix.R (graphNEL -> Tsparse): method for weight case.
1487 :     (Tsp2grNEL): other fixes needed
1488 :    
1489 : maechler 1548 2006-09-11 Martin Maechler <maechler@stat.math.ethz.ch>
1490 :    
1491 :     * R/AllClass.R ("nMatrix"): and subclasses for "nonzero pattern"
1492 :     Matrices, since "lMatrix", also "lsparseM" can have NA
1493 :     * R/ndenseMatrix.R, etc: new source files
1494 :     * man/nsparseMatrix-classes.Rd, etc: new help files
1495 :     * tests/: adaptions
1496 :     * src/chm_common.c (chm_dense_to_SEXP): and others:
1497 :     new 'Rkind' argument: "l*" and "d*" both use CHOLMOD_REAL
1498 : maechler 1582 * src/Csparse.c, etc: ditto
1499 : maechler 1548
1500 : bates 1546 2006-09-11 Douglas Bates <bates@R-project.org>
1501 :    
1502 :     * src/Mutils.[ch],init.c inst/include/*.h: Move the
1503 :     alloc_d**Matrix functions to the lme4 package.
1504 :    
1505 : bates 1543 2006-09-09 Douglas Bates <bates@R-project.org>
1506 :    
1507 :     * src/dsCMatrix.c (dsCMatrix_Cholesky): igoring LDL = FALSE now
1508 : maechler 1544 fixed
1509 : bates 1543
1510 : maechler 1544 2006-09-09 Martin Maechler <maechler@stat.math.ethz.ch>
1511 :    
1512 : maechler 1548 * R/lMatrix.R: new
1513 :    
1514 : maechler 1544 * R/sparseMatrix.R (Tsp2grNEL): do not yet use graph::foo()
1515 :    
1516 :     * R/dgeMatrix.R: do not define tcrossprod() methods for "matrix"
1517 : maechler 1582 * man/tcrossprod.Rd: ditto
1518 : maechler 1544
1519 : bates 1538 2006-09-08 Douglas Bates <bates@stat.wisc.edu>
1520 :    
1521 :     * inst/include/Matrix_stubs.c,Matrix.h: Add declarations and stubs
1522 :     for exported functions
1523 :     * src/Makefile, src/CHOLMOD/Lib/Makefile, src/Metis,CAMD,CCOLAMD:
1524 :     Remove partitioning algorithms for sparse matrix reordering. The
1525 :     copyright on the Metis code was problematic and the methods were
1526 :     rarely used.
1527 :     * src/triplet_to_col.[ch],MMHB.[ch]: Remove triplet_to_col. Such
1528 :     operations are now done entirely in CHOLMOD code.
1529 :    
1530 : bates 1517 2006-09-06 Douglas Bates <bates@R-project.org>
1531 :    
1532 :     * src/Mutils.h: Remove functions that are no longer used.
1533 :    
1534 : bates 1507 2006-09-04 Douglas Bates <bates@R-project.org>
1535 :    
1536 :     * src/dtCMatrix.c (dtCMatrix_validate): rename functions.
1537 :     * src/DEPS.mkf: update
1538 :    
1539 : maechler 1481 2006-09-02 Martin Maechler <maechler@stat.math.ethz.ch>
1540 :    
1541 :     * created branches/Matrix-for-R-2.3.x; on trunk: do
1542 :     * DESCRIPTION (Version): 0.9975-0
1543 :     (Depends): R (>= 2.4.0)
1544 :    
1545 : bates 1475 2006-09-01 Douglas Bates <bates@R-project.org>
1546 :    
1547 :     * R/sparseMatrix.R: Added direct method to CsparseMatrix from graphNEL
1548 :    
1549 : maechler 1472 2006-09-01 Martin Maechler <maechler@stat.math.ethz.ch>
1550 :    
1551 :     * R/sparseMatrix.R: add coercion from "ANY" to "sparseMatrix"
1552 :     * R/denseMatrix.R: add coercion from "ANY" to "denseMatrix"
1553 :    
1554 :     * R/Matrix.R ([): use nargs() to disambiguate M[i] and M[i,]
1555 :    
1556 :     2006-08-31 Martin Maechler <maechler@stat.math.ethz.ch>
1557 :    
1558 :     * R/sparseMatrix.R (Arith): moved Arith group method one-level up
1559 :     from "dsparse" to "sparse" and now go via "Csparse" instead of "dgC"
1560 : maechler 1582 * R/dsparseMatrix.R: ditto
1561 :     * R/Csparse.R: ditto
1562 : maechler 1472
1563 :     2006-08-31 Martin Maechler <maechler@stat.math.ethz.ch>
1564 :    
1565 :     * R/dMatrix.R (Compare): improve availability of "<", etc
1566 :     * R/Auxiliaries.R (asTuniq): new; also make use of R 2.4.x print(*,max)
1567 :    
1568 : maechler 1467 2006-08-30 Martin Maechler <maechler@stat.math.ethz.ch>
1569 :    
1570 :     * R/dgCMatrix.R: aargh: "Arith(<dgC>, numeric)" was wrong because
1571 :     of a 0-index which was used as 1-index (..hmm)
1572 :    
1573 :     * R/sparseMatrix.R (prSpMatrix): fix printing an all-0 sparse Matrix
1574 :    
1575 :     * R/Auxiliaries.R (all0, is0): for 0-testing in presence of NA's
1576 :     * R/Auxiliaries.R (isTriMat): use all0() for 0-testing.
1577 : maechler 1582 (.is.diagonal): ditto
1578 : maechler 1467
1579 :     * R/lgTMatrix.R: as("matrix", "lgTMatrix"): warn about NA's
1580 :    
1581 :     * R/Matrix.R (Matrix): also work for NA data
1582 :    
1583 : maechler 1455 2006-08-28 Martin Maechler <maechler@stat.math.ethz.ch>
1584 :    
1585 :     * R/Matrix.R (Matrix): + 'forceCheck' argument; dimnames setting
1586 :     in all cases.
1587 :    
1588 : bates 1453 2006-08-27 Douglas Bates <bates@R-project.org>
1589 :    
1590 :     * src/dense.[ch],init.c, R/ddenseMatrix.R, man/band.Rd
1591 :     (ddense_band): Added triu, tril and band for ddenseMatrix objects.
1592 :    
1593 : maechler 1447 2006-08-25 Martin Maechler <maechler@stat.math.ethz.ch>
1594 :    
1595 :     * src/Mutils.c (dup_mMatrix_as_dgeMatrix): added all subclasses of
1596 :     subclasses of "ddenseMatrix"
1597 :     * src/init.c et al: outcomment dtrM*_as_dge* and dsyM*_as_dge*_
1598 :     * R/ddenseMatrix.R et al: setAs("ddenseMatrix", "dgeMatrix", ..)
1599 :     instead of half dozen specialized ones.
1600 :    
1601 : bates 1445 2006-08-25 Douglas Bates <bates@R-project.org>
1602 :    
1603 :     * R/lmer.R (qqmath method): Bug fix provided by Emmanuel Tillard
1604 :     <tillard@cirad.fr> - ordering standard errors to match effects.
1605 :    
1606 : bates 1439 2006-08-24 Douglas Bates <bates@R-project.org>
1607 : bates 1431
1608 : bates 1439 * src/lsCMatrix.c (lsCMatrix_trans): Remove lsCMatrix_chol based
1609 :     on R_ldl.
1610 :     * R/lCholCMatrix.R,
1611 :     src/[dl]CholCMatrix.[ch],R_ldl.[ch],Metis_utils.[ch]: removed
1612 :     * src/dsCMatrix.c (dsCMatrix_to_dgTMatrix): use CHOLMOD
1613 :     * many files in ./R and ./src: Use more general version of
1614 :     dup_mMatrix_as_dgeMatrix to simplify method definitions.
1615 : bates 1442 * src/Mutils.c (dup_mMatrix_as_dgeMatrix): Add ddiMatrix,
1616 :     dtpMatrix, dspMatrix and dppMatrix conversions.
1617 :    
1618 : maechler 1447
1619 : bates 1439 2006-08-23 Douglas Bates <bates@R-project.org>
1620 :    
1621 :     * R/AllClass.R,lCholCMatrix.R,src/SOURCES_C.mkf,init.c,NAMESPACE:
1622 :     Remove classes lCholCMatrix and dCholCMatrix based on R_ldl code.
1623 : bates 1431 * src/dgeMatrix.c: Ensure 'factors' slot exists in result of
1624 :     dgeMatrix_crossprod (may need to do this in other places).
1625 :     * R/AllGeneric.R,dsCMatrix.R, src/dscMatrix.[ch]: Add Cholesky
1626 :     generic and method for dsCMatrix. Use CHOLMOD for chol().
1627 :    
1628 : bates 1414 2006-08-22 Douglas Bates <bates@R-project.org>
1629 :    
1630 :     * src/Mutils.c (dup_mMatrix_as_dgeMatrix): updated for general
1631 :     types of classed Matrices, matrices or numeric or logical vectors.
1632 : bates 1423 * src/init.c: register dup_mMatrix_as_dgeMatrix for coercions.
1633 :     * src/chm_common.c,Mutils.h (as_cholmod_factor): Move check_class
1634 :     to Mutils.h (as an inline) and change name to Matrix_check_class;
1635 :     fixes in as_cholmod_factor and chm_factor_to_SEXP.
1636 :     * src/dsCMatrix.[ch]: Use CHOLMOD for dsCMatrix_chol and
1637 :     dsCMatrix_matrix_solve. Comment out vestigial functions.
1638 :     * src/Csparse.c: use diag_P and uplo_P macros.
1639 : maechler 1447
1640 : bates 1405 2006-08-21 Douglas Bates <bates@R-project.org>
1641 :    
1642 :     * src/lmer.c (internal_mer_RZXinv): Fix memory leak caught by
1643 : maechler 1447 valgrind.
1644 : bates 1411 * tests/matprod.R: Add tests to verify that 'solve' and '%*%' are
1645 :     inverses.
1646 :     * src/sparseQR.c (sparseQR_validate): add new validation test, fix
1647 :     -Wall warnings.
1648 :     * src/dppMatrix.c,dtrMatrix.c,dgCMatrix.c,dgeMatrix.c,dspMatrix.c:
1649 :     Use dup_mMatrix_as_dgeMatrix.
1650 : maechler 1447
1651 : bates 1403 2006-08-20 Douglas Bates <bates@R-project.org>
1652 :    
1653 :     * src/sparseQR.c: Fix thinko in sparseQR_resid_fitted.
1654 :     * tests/sparseQR.R: Added
1655 :     * man/sparseQR-class.Rd: Document methods for qr.* generics
1656 :     * R/sparseQR.R: Return correct # of coefs; fix cut-and-paste errors
1657 :    
1658 : bates 1398 2006-08-19 Douglas Bates <bates@R-project.org>
1659 :    
1660 :     * NAMESPACE, R/sparseQR.R, src/init.c,sparseQR.[ch],SOURCES_C.mkf:
1661 :     Added methods for sparseQR for qr.qy, qr.qty, qr.coef, qr.resid
1662 :     and qr.fitted.
1663 :     * src/Mutils.[ch]: Added dup_mMatrix_as_dgeMatrix utility
1664 :     * src/dgCMatrix.c: Check for ordering before storing q in dgCMatrix_QR
1665 :    
1666 : maechler 1389 2006-08-18 Martin Maechler <maechler@stat.math.ethz.ch>
1667 :    
1668 :     * R/AllGeneric.R: add "qr" and "chol" generics; via 'trick' since
1669 :     the base version has no "..." argument.
1670 :    
1671 :     * R/sparseMatrix.R (prSpMatrix): fix the triangular unit diagonal case.
1672 :    
1673 :     * R/Matrix.R: define and
1674 :     * NAMESPACE: export as.numeric() and as.logical() methods.
1675 :     Let's hope these do not badly slow down something...
1676 :     Finally export the zapsmall() method.
1677 :    
1678 : bates 1388 2006-08-17 Douglas Bates <bates@R-project.org>
1679 :    
1680 :     * src/dgCMatrix.[ch] (dgCMatrix_matrix_solve), src/init.c,
1681 :     R/dgCMatrix.R: solve methods for dgCMatrix and dense RHS.
1682 :     * src/dtCMatrix.c :Remove code that is no longer used
1683 :     * R/dtCMatrix.R: Use C code for diagU2N in CsparseMatrix classes
1684 :    
1685 : bates 1370 2006-08-14 Douglas Bates <bates@R-project.org>
1686 :    
1687 : bates 1373 * src/Csparse.[ch],init.c (Csparse_to_logical): Added utilities
1688 :     Csparse_to_logical and Csparse_symmetric_to_general.
1689 :     * R/dgCMatrix.R,dsCMatrix.R,Csparse.R : Consolidate general
1690 : maechler 1389 coercion methods between CsparseMatrix and TsparseMatrix.
1691 : bates 1373
1692 :     2006-08-14 Douglas Bates <bates@R-project.org>
1693 :    
1694 : bates 1370 * R/dtCMatrix.R,dgCMatrix.R,Csparse.R src/init.c,dgCMatrix.[ch],
1695 :     Csparse.[ch],chm_common.c,dense.c : Use CHOLMOD code and methods
1696 :     for CsparseMatrix, TsparseMatrix, denseMatrix or matrix when
1697 :     possible.
1698 :    
1699 : bates 1368 2006-08-12 Douglas Bates <bates@R-project.org>
1700 :    
1701 :     * src/chm_common.[ch],Csparse.[ch],Tsparse.[ch],CHMfactor.c,dtTMatrix.c,
1702 :     dgTMatrix.c,dgCMatrix.c,dsCMatrix.c,dtTMatrix.c, R/dsTMatrix.R,
1703 :     Tsparse.R,Csparse.R,dgTMatrix.R,dsCMatrix.R,lsCMatrix.R:
1704 :     generalize conversions between TsparseMatrix, CsparseMatrix,
1705 :     denseMatrix and matrix. Preserve triangularity property and
1706 :     propagate Dimnames in the easy cases.
1707 :    
1708 : bates 1365 2006-08-10 Douglas Bates <bates@R-project.org>
1709 :    
1710 :     * src/lmer.c: adjust checks in glmer_init for S4SXP
1711 :     * tests/validObj.R: check of all(eq) should be all(eq@x) - worked
1712 :     before S4SXP but for the wrong reasons.
1713 :    
1714 : bates 1354 2006-08-08 Douglas Bates <bates@R-project.org>
1715 :    
1716 : bates 1360 * src/Csparse.c (Csparse_crossprod): tcrossprod result has stype = -1.
1717 :     Later modified to return the upper triangle only.
1718 :     * R/dgTMatrix.R: Remove vestigial crossprod and tcrossprod methods.
1719 : maechler 1389
1720 : bates 1352 2006-08-07 Douglas Bates <bates@R-project.org>
1721 :    
1722 :     * src/Csparse.c (Csparse_crossprod): Set stype on result to avoid
1723 :     R-level conversion to a sparse symmetric class.
1724 :     * R/Tsparse.R,R/Csparse.R (crossprod and tcrossprod methods):
1725 :     Remove conversion to sparse symmetric classes (now done in C code).
1726 :    
1727 : maechler 1349 2006-08-07 Martin Maechler <maechler@stat.math.ethz.ch>
1728 :    
1729 : maechler 1351 * R/dgCMatrix.R: disable old crossprod and tcrossprod methods
1730 :     * man/band.Rd: adapt the \dontshow{} unit test.
1731 :    
1732 :     2006-08-07 Martin Maechler <maechler@stat.math.ethz.ch>
1733 :    
1734 : maechler 1349 * DESCRIPTION (Version): 0.995-14 for CRAN
1735 :    
1736 :     * tests/other-pkgs.R: oops: library(Matrix) outside *if* !
1737 :    
1738 :     * R/sparseMatrix.R (Tsp2grNEL): fixed Tsparse -> graph coercion
1739 :     * tests/other-pkgs.R: more checks, sparseMatrix -> graph
1740 :    
1741 :     * R/Auxiliaries.R (as_Tsparse, as_Rsparse): new
1742 :     * R/Tsparse.R (tril, triu, band): methods
1743 : bates 1352 * R/dgRMatrix.R (tril, ...): ditto
1744 :     * man/band.Rd: ditto
1745 : maechler 1349
1746 :     2006-08-04 Martin Maechler <maechler@stat.math.ethz.ch>
1747 :    
1748 :     * R/Matrix.R (head, tail): directly use utils:::head.matrix
1749 :     to be up-to-date automatically.
1750 :    
1751 : maechler 1346 2006-08-03 Martin Maechler <maechler@stat.math.ethz.ch>
1752 :    
1753 :     * DESCRIPTION (Version): 0.995-13 to be released to CRAN
1754 :    
1755 :     * DESCRIPTION (Lazydata): no, instead of 'yes' because it fails for:
1756 :     * data/CAex.R, inst/external/CAex_slots.rda: replacing data/CAex.rda
1757 :     * data/KNex.R, inst/external/KNex_slots.rda: replacing data/KNex.rda
1758 :     such that the S4 objects are always created by the current version
1759 :     of R and 'Matrix' class definitions.
1760 :    
1761 : bates 1342 2006-08-01 Douglas Bates <bates@R-project.org>
1762 :    
1763 :     * R/lmer.R (LMEoptimize method), tests/lmer.R,
1764 : maechler 1346 inst/external/test3comp.rda: Added warnings for convergence on
1765 : bates 1342 boundary and test cases.
1766 :    
1767 :     * src/lmer.c (mer_postVar): Modified to return the variances that
1768 :     are marginal to the fixed effects, not conditional on them (which
1769 :     is what the bVar slot contents represent).
1770 :    
1771 : bates 1338 2006-07-31 Douglas Bates <bates@R-project.org>
1772 :    
1773 :     * NAMESPACE, src/lmer.c, R/lmer.R (hatTrace): Add the hatTrace
1774 :     function which calls the C function mer_hat_trace2.
1775 : maechler 1346
1776 : bates 1342 * man/ranef.Rd: Include description of "postVar" argument and
1777 :     producing a caterpillar plot.
1778 : bates 1338
1779 : maechler 1335 2006-07-31 Martin Maechler <maechler@stat.math.ethz.ch>
1780 :    
1781 :     * NAMESPACE: change "correlation" to "corMatrix"
1782 :     * R/AllClass.R: to avoid clash with S3 class in 'nlme'.
1783 : bates 1352 * R/dpoMatrix.R: ditto
1784 :     * R/lmer.R: ditto
1785 : maechler 1335
1786 : bates 1338 2006-07-28 Douglas Bates <bates@R-project.org>
1787 :    
1788 :     * src/lmer.c (internal_mer_RZXinv): Split the calculation of the
1789 :     RZXinv slot's contents into a separate internal function that can
1790 :     be used in mer_hat_trace.
1791 :    
1792 : maechler 1331 2006-07-22 Martin Maechler <maechler@stat.math.ethz.ch>
1793 :    
1794 :     * R/Matrix.R: Coercions "Matrix" -> (sparse|dense)Matrix
1795 :     via new smart
1796 :     * R/Auxiliaries.R (as_Csparse, as_dense, .M.shapse): new
1797 :     utility functions.
1798 :    
1799 :    
1800 : maechler 1330 2006-07-21 Martin Maechler <maechler@stat.math.ethz.ch>
1801 :    
1802 : maechler 1331 * R/Csparse.R (tril, triu, band): do return *triangular* classed
1803 :     matrices when appropriate; band() even symmetric ones.
1804 :     (replCmat): extend to potentially all "CsparseMatrix"
1805 :     * R/Tsparse.R (replTmat): extend to all "TsparseMatrix"; hence
1806 :     allow subassignment for special sparse matrices.
1807 :    
1808 :     * R/Auxiliaries.R (as_geClass): factor out the .M.kind() functionality
1809 :    
1810 : maechler 1330 * src/lmer.c (mer_MCMCsamp, glmer_MCMCsamp): new 'verbose'
1811 :     argument; in glmer_*(): print only if(verbose).
1812 :    
1813 :     speed-optimize a few places by moving REAL(.) out of loops.
1814 :    
1815 :     * src/lmer.h, src/init.h, R/lmer.R: related to above.
1816 :    
1817 : maechler 1329 2006-07-20 Martin Maechler <maechler@stat.math.ethz.ch>
1818 :    
1819 :     * R/Matrix.R("["): disable ("Matrix", i = "logical", j = "missing"),
1820 :     since that wrongly triggers also for M[ logi , ]
1821 :    
1822 :     * R/denseMatrix.R: "[" methods now also work e.g. when indexing
1823 :     a symmetric matrix that results in a non-symmetric one.
1824 :     * R/Auxiliaries.R (as_geClass): new function used in "[" above.
1825 :    
1826 :     * R/dMatrix.R: make round(M) work as round(M, 0)
1827 :    
1828 :     * R/dgTMatrix.R (image): coordinate system and axis now use
1829 :     1-based indices, not 0-based ones.
1830 :    
1831 :     * R/Tsparse.R (.ind.prep for "["): get rid of max(<empty>) warning.
1832 :     * tests/indexing.R: test it.
1833 :    
1834 :     * NAMESPACE: export isSymmetric(); has been a generic in "base" for a while;
1835 :     * man/isSymmetric-methods.Rd: and document it.
1836 :    
1837 :     * R/SparseM-conv.R: added coercion methods for some 'SparseM' matrices.
1838 :     * man/SparseM-conv.Rd: docu them
1839 :    
1840 :     * tests/other-pkgs.R: renamed from tests/graph.R and add example
1841 :     for 'SparseM' conversions
1842 :    
1843 :     2006-07-17 Douglas Bates <Douglas.Bates@R-project.org>
1844 :    
1845 :     * R/Matrix.R (head): added head() and tail() methods.
1846 :    
1847 :     2006-07-17 Martin Maechler <maechler@stat.math.ethz.ch>
1848 :    
1849 :     * DESCRIPTION (Version): 0.995-12 released to CRAN
1850 :    
1851 : maechler 1319 2006-07-15 Martin Maechler <maechler@stat.math.ethz.ch>
1852 :    
1853 :     * tests/simple.R: add check for correct dsT -> dgT coercion;
1854 :     add check for correct printing of symmetric sparse matrices.
1855 :    
1856 :     * R/Auxiliaries.R (non0ind): return *all* non-0 entry indices also
1857 :     for sparse symmetric matrices.
1858 :    
1859 :     * src/dsTMatrix.c (dsTMatrix_as_dgTMatrix): do not copy the
1860 :     diagonal twice.
1861 :    
1862 : bates 1316 2006-07-11 Douglas Bates <Douglas.Bates@R-project.org>
1863 :    
1864 :     * src/dsTMatrix.c (dsTMatrix_as_dgTMatrix): Fix a case of INTEGER
1865 : maechler 1319 being applied to the x slot (detected by Brian Ripley).
1866 : bates 1316
1867 : maechler 1315 2006-07-10 Martin Maechler <maechler@stat.math.ethz.ch>
1868 :    
1869 :     * src/dgCMatrix.c (dgCMatrix_validate): 'p' slot must have correct length.
1870 :    
1871 :     * R/Auxiliaries.R (isTriC): fix buglet (we were 1-based!)
1872 :    
1873 :     2006-07-08 Martin Maechler <maechler@stat.math.ethz.ch>
1874 :    
1875 :     * src/lgCMatrix.c (lgCMatrix_diag): new function
1876 :     * R/lgCMatrix.R (diag): for new method
1877 :    
1878 :     * R/AllClass.R (TsparseMatrix): do use Tsparse_validate
1879 :     ==> construction of illegal "*gTMatrix" via new() should
1880 :     now be much less easy:
1881 :     * tests/Class+Meth.R: assertError() for some illegal "dgT*"
1882 :    
1883 :     * R/Matrix.R (Matrix): Matrix(0, nrow,ncol) now "goes sparse"
1884 :     directly.
1885 :     * man/Matrix.Rd: documents it.
1886 :    
1887 : bates 1311 2006-07-06 Douglas Bates <bates@R-project.org>
1888 :    
1889 :     * src/pedigree.c (pedigree_inbreeding): Correction in
1890 :     initialization. This function is not currently being used and is
1891 :     not fully tested.
1892 :    
1893 : bates 1312 * NAMESPACE, R/{AllClass.R,lmer.R}, src/{init.c,lmer.c}:
1894 :     Introduced the glmer class. Added code for mcmcmsamp on glmer
1895 :     objects. Modified validity check on pedigree objects to account
1896 :     for nonparallel patterns of missingness of parents.
1897 : bates 1311
1898 : bates 1313 * man/{lmer-class.Rd,mcmcsamp.Rd}: Update documentation for glmer
1899 :     class.
1900 : maechler 1315
1901 :     2006-07-01 Martin Maechler <maechler@stat.math.ethz.ch>
1902 :    
1903 :     * R/pMatrix.R: coercion pMatrix -> Tsparse
1904 :    
1905 : bates 1300 2006-06-12 Douglas Bates <bates@R-project.org>
1906 :    
1907 : maechler 1319 * DESCRIPTION (Version): 0.995-11 released to CRAN
1908 :    
1909 : bates 1300 * R/lmer.R (mcmcsamp method): Corrected arrangments of names on
1910 :     the output from mcmcsamp.
1911 :    
1912 : bates 1298 2006-06-10 Douglas Bates <bates@R-project.org>
1913 :    
1914 : bates 1300 * R/lmer.R (simulestimate): added C code for calculating the trace
1915 :     of the hat matrix.
1916 : bates 1298
1917 : maechler 1295 2006-06-09 Martin Maechler <maechler@stat.math.ethz.ch>
1918 :    
1919 :     * R/diagMatrix.R (setAs): define coercion methods to sparse matrix
1920 :     classes.
1921 : maechler 1315 * R/sparseMatrix.R etc: multiplication of diagonal and sparse
1922 : maechler 1295
1923 : maechler 1290 2006-06-08 Martin Maechler <maechler@stat.math.ethz.ch>
1924 :    
1925 :     * R/dgTMatrix.R (colSums): etc. All four of
1926 :     colSums(), rowSums(), colMeans(), rowMeans() now should work for
1927 :     all "Matrices".
1928 :    
1929 : bates 1288 2006-06-01 Douglas Bates <bates@stat.wisc.edu>
1930 :    
1931 :     * R/lmer.R (panel.ci): Add a reference line at zero and a
1932 :     background grid to the qqmath plot of ranef.lmer.
1933 :    
1934 : bates 1287 2006-05-30 Douglas Bates <bates@stat.wisc.edu>
1935 : bates 1284
1936 : bates 1287 * R/lmer.R (expandSlash): Functions (non-exported) to allow nested
1937 :     grouping factors to be specified in the formula as (1|foo/bar).
1938 :    
1939 :     2006-05-27 Douglas Bates <bates@stat.wisc.edu>
1940 :    
1941 : bates 1284 * R/lmer.R (findbars and others): Change check of is.numeric to
1942 :     !is.language to resolve the bug reported by Jacob Wegelin.
1943 :    
1944 :     * src/pedigree.c (pedigree_inbreeding): Initial implementation of
1945 :     code to evaluate inbreeding coefficients without calculating T,
1946 :     based on code in Sargolzaei and Iwaisaki's paper.
1947 :    
1948 : bates 1283 2006-05-27 Douglas Bates <bates@stat.wisc.edu>
1949 :    
1950 :     * R/{lmer.R,AllGeneric.R}, src/{init.c,lmer.[ch]}: Added local
1951 :     generic and mer methods for isNested and denomDF. This denomDF was
1952 :     an attempt to emulate that in lme but I don't think that makes
1953 :     sense. Use the trace of the hat matrix instead.
1954 :    
1955 : maechler 1271 2006-05-17 Martin Maechler <maechler@stat.math.ethz.ch>
1956 :    
1957 :     * R/sparseMatrix.R: Matrix <-> graph methods: can no longer use
1958 :     the C code depending on a slot structure that's no longer valid.
1959 : bates 1352 * src/dgTMatrix.c: ditto (also: src/init.c src/dgTMatrix.h)
1960 : maechler 1271
1961 :    
1962 : bates 1268 2006-05-17 Douglas Bates <bates@stat.wisc.edu>
1963 :    
1964 :     * R/{AllGeneric.R,Csparse.R},man/band.Rd,NAMESPACE: changed name
1965 :     of lowerTriMatrix generic and methods to tril (also upper to triu)
1966 :     and added a general band extractor.
1967 :    
1968 : bates 1267 2006-05-16 Douglas Bates <bates@stat.wisc.edu>
1969 :    
1970 :     * R/pedigree.R (pedigree): Replace sire and dam values outside the
1971 :     allowable range with NAs. Added a corresponding check in the
1972 :     validity check for the pedigree class.
1973 :    
1974 :     * R/[CT]sparse.R ([t]crossprod): The result of single-argument
1975 :     crossprod methods now inherits from symmetricMatrix.
1976 :    
1977 : bates 1265 2006-05-15 Douglas Bates <bates@stat.wisc.edu>
1978 :    
1979 :     * R/AllGeneric.R (lowerTriMatrix): Added (but did not export)
1980 :     generics lowerTriMatrix and upperTriMatrix along with methods for
1981 :     the Csparse virtual class. Also added a C function Csparse_band
1982 :     that implements these methods by calling cholmod_band.
1983 :    
1984 : maechler 1264 2006-05-15 Martin Maechler <maechler@stat.math.ethz.ch>
1985 :    
1986 :     * R/Tsparse.R ("["): column or row subsetting; @Dimnames[k] got
1987 :     erased when it was NULL. This led to invalid subselections!
1988 :    
1989 : bates 1259 2006-04-25 Douglas Bates <bates@stat.wisc.edu>
1990 :    
1991 :     * R/dtCMatrix.R: avoid coercion of dtCMatrix object to dgCMatrix
1992 :     in method for "t" so as not to lose the unit diagonal property.
1993 :    
1994 : bates 1257 2006-04-19 Douglas Bates <bates@stat.wisc.edu>
1995 :    
1996 :     * R/lmer.R, R/AllGeneric.R, NAMESPACE: Remove the postVar generic
1997 :     and methods. This is now an option to the ranef method for the
1998 :     mer class.
1999 :    
2000 :     * src/cs_utils.c: Ensure that the nz component is -1 for a
2001 :     compressed column-oriented matrix. Minor formatting cleanup.
2002 :    
2003 :     * man/lmer-class.Rd: Document the qqmath method for ranef.lmer
2004 :     objects.
2005 :    
2006 : maechler 1253 2006-04-19 Martin Maechler <maechler@stat.math.ethz.ch>
2007 :    
2008 :     * R/Auxiliaries.R (diagU2N): new for the solve() methods in
2009 :     * R/dtCMatrix.R: where dgC -> dgT coercion now preserves diag = "U".
2010 :    
2011 : bates 1251 2006-04-15 Douglas Bates <bates@stat.wisc.edu>
2012 :    
2013 :     * src/cs.[ch],src/cs_utils.[ch] : Added Tim Davis' CSparse library
2014 :     in cs.[ch] and utilities to interface to that code in cs_utils.[ch].
2015 :    
2016 :     * R/dtCMatrix.R, src/dtCMatrix.[ch] : CSparse-based solve methods
2017 :     for the dtCMatrix class.
2018 : maechler 1253
2019 : bates 1247 2006-04-12 Douglas Bates <bates@stat.wisc.edu>
2020 :    
2021 :     * R/pedigree.R, R/AllClass.R, NAMESPACE: added a pedigree class
2022 :     and methods for it.
2023 :    
2024 : maechler 1245 2006-04-12 Martin Maechler <maechler@stat.math.ethz.ch>
2025 :    
2026 :     * R/dgCMatrix.R: add storage.mode(.) <- "double" for "matrix"
2027 :     arguments, such that M %*% 1:6 now works
2028 :     * Tests/matprod.R: test the above
2029 :    
2030 : bates 1244 2006-04-03 Douglas Bates <bates@stat.wisc.edu>
2031 : bates 1243
2032 :     * R/lmer.R (qqmath,ranef.lmer-method): added a qqmath method for
2033 :     the ranef.lmer class.
2034 :    
2035 :     * R/AllClass.R, NAMESPACE, R/lmer.R: Added a postVar generic and
2036 :     methods to extract the posterior variances from the bVar slot.
2037 :    
2038 : maechler 1238 2006-03-30 Martin Maechler <maechler@stat.math.ethz.ch>
2039 :    
2040 :     * R/dtCMatrix.R: allow coercion from dgC* to triangular (dtC*)
2041 :     * R/dsCMatrix.R: and symmetric (dsC*) 'Csparse' matrices.
2042 :    
2043 :     * R/Tsparse.R: Tsparse* -> Csparse* coercion now works and is tested in
2044 :     * tests/simple: (extended)
2045 :    
2046 :     * R/sparseMatrix.R (isTriangular): now using much improved
2047 :     * R/Auxiliaries.R (isTriC): new triangularity check for *CMatrix
2048 :    
2049 : bates 1236 2006-03-23 Douglas Bates <bates@stat.wisc.edu>
2050 :    
2051 :     * src/dsyMatrix.c (dsyMatrix_as_dspMatrix): Propagate DimNames
2052 :     (problem report from Franklin Parlamis). This should be done
2053 : maechler 1238 generally.
2054 : bates 1236
2055 : bates 1234 2006-03-21 Douglas Bates <bates@stat.wisc.edu>
2056 :    
2057 :     * R/AllClass.R,lmer.R: Change the name of the lmer.ranef class to
2058 :     ranef.lmer (like summary.lmer). Add the coef.lmer class and
2059 :     update the plot methods.
2060 :    
2061 : bates 1232 2006-03-20 Douglas Bates <bates@stat.wisc.edu>
2062 :    
2063 :     * R/lmer.R (resid and ranef methods): Added methods for the
2064 :     "residuals" and "resid" generic but only for linear mixed model
2065 :     fits. Changed the ranef method to return a list of data frames so
2066 :     that the plot methods now work.
2067 :    
2068 : bates 1230 2006-03-16 Douglas Bates <bates@bates2>
2069 :    
2070 :     * src/dpoMatrix.c (dpoMatrix_chol): Require n > 0 in call to
2071 :     dpotrf - otherwise the BLAS on Mac OS X complains and quits.
2072 :    
2073 :     * DESCRIPTION (Date): New release
2074 :    
2075 : maechler 1228 2006-03-15 Martin Maechler <maechler@stat.math.ethz.ch>
2076 :    
2077 :     * DESCRIPTION (Version): 0.995-6 -- to be released to CRAN
2078 :    
2079 :     * data/KNex.rda: replacing 'mm' and 'y' by KNex <- list(mm=mm, y=y)
2080 :     * man/KNex.Rd: and other help files
2081 :     * tests/*.R: several ones needed adaption
2082 : bates 1352 * inst/doc/Comparisons.Rnw: ditto
2083 : maechler 1228
2084 : maechler 1226 2006-03-11 Martin Maechler <maechler@stat.math.ethz.ch>
2085 :    
2086 :     * R/dgCMatrix.R (replCmat): "[<-" methods for dgCMatrix
2087 :    
2088 :     * tests/indexing.R: tests for new [<- methods for sparse matrices.
2089 :    
2090 :     2006-03-10 Martin Maechler <maechler@stat.math.ethz.ch>
2091 :    
2092 :     * R/dgTMatrix.R (replTmat): "[<-" methods for dgTMatrix
2093 :    
2094 :     * R/Tsparse.R (.ind.prep): fix out-of-range indexing
2095 :    
2096 :     2006-03-08 Martin Maechler <maechler@stat.math.ethz.ch>
2097 :    
2098 :     * R/dMatrix.R: enable things like M [ M < 10 ]
2099 :     * R/dgeMatrix.R: implement it
2100 :    
2101 : maechler 1222 2006-03-06 Martin Maechler <maechler@stat.math.ethz.ch>
2102 :    
2103 :     * R/AllClass.R: define "summary.mer" and "*.lmer"
2104 :     * R/lmer.R (summary): summary(<mer>) computes & returns the above;
2105 :     * R/lmer.R (show): now works with summary()
2106 :    
2107 :     2006-03-04 Martin Maechler <maechler@stat.math.ethz.ch>
2108 :    
2109 :     * R/dgCMatrix.R: finally direct "Arith" dgC o dgC
2110 :     * R/Auxiliaries.R (WhichintersectInd): and other utilities to
2111 :     support the above
2112 :    
2113 : bates 1213 2006-02-07 Douglas Bates <bates@stat.wisc.edu>
2114 :    
2115 :     * R/lmer.R (lmer): fix initial values of offset and weights for glm.fit.
2116 :     Use glmFit$prior.weights for weights in a glmm.
2117 :     Allow an option usePQL = FALSE to skip the PQL steps for the
2118 :     Laplace method (and, in time, the AGQ method).
2119 :    
2120 :     * src/lmer.c (mer_factor): Move downdating and factoring of XtX
2121 :     into a separate function internal_mer_Xfactor to be able to call
2122 :     it from internal_bhat.
2123 :    
2124 : maechler 1200 2006-01-23 Martin Maechler <maechler@stat.math.ethz.ch>
2125 :    
2126 :     * tests/Class+Meth.R (tstMatrixClass): function for much better
2127 :     testing; now again of all actual classes.
2128 :    
2129 :     * src/Mutils.c (MAKE_TRIANGULAR_BODY, MAKE_SYMMETRIC_BODY):
2130 :     use macros and define make_d_matrix_* and make_i_matrix_*
2131 :     where _i_ is for the ldense routines:
2132 :    
2133 :     * src/ldense.c (ltrMatrix_as_lgeMatrix): provide functions
2134 :     * src/ldense.c (lsyMatrix_as_lgeMatrix):
2135 :    
2136 :     * R/ldenseMatrix.R: use the above in setAs(*,"lgeMatrix")
2137 :    
2138 :    
2139 : maechler 1174 2006-01-16 Martin Maechler <maechler@stat.math.ethz.ch>
2140 :    
2141 :     * R/Matrix.R (Matrix): has become much "smarter" now auto-producing
2142 :     many different kinds of matrices.
2143 :     * R/*.R: quite a few new methods were needed for R CMD check with
2144 :     new Matrix(). Very good for users playing around.
2145 :    
2146 :    
2147 : maechler 1165 2006-01-15 Martin Maechler <maechler@stat.math.ethz.ch>
2148 :    
2149 :     * src/dgeMatrix.c (dMatrix_validate): new
2150 :     * src/Mutils.c (dense_nonpacked_validate): new
2151 :    
2152 :     * src/dtrMatrix.c (dtrMatrix_validate): improved/fixed
2153 :    
2154 :    
2155 :     2006-01-14 Douglas Bates <bates@stat.wisc.edu>
2156 :    
2157 :     * R/AllClass.R (compMatrix), (generalMatrix): new virtual classes
2158 :    
2159 : bates 1123 2006-01-07 Douglas Bates <bates@stat.wisc.edu>
2160 : bates 1119
2161 : maechler 1127 * DESCRIPTION (Version): 0.99-6 released to CRAN
2162 :    
2163 : bates 1119 * src/dgBCMatrix.c (cscb_trcbsm): Fix due to Peter Dalgaard for
2164 :     segfault in cases with multiple non-nested grouping factors.
2165 :    
2166 : maechler 1109 2006-01-03 Martin Maechler <maechler@stat.math.ethz.ch>
2167 :    
2168 :     * DESCRIPTION (Version): 0.99-4 to be released to CRAN
2169 :     (Depends): also on 'utils'
2170 :    
2171 :     * R/AllClass.R (diagonalMatrix): new class with "ddi*" and "ldi*"
2172 :     * R/diagMatrix.R (Diagonal): constructor and methods for
2173 :     diagonal matrices
2174 :    
2175 :     * R/ltTMatrix.R: new "minimal methods"
2176 :    
2177 : maechler 1091 2005-12-12 Martin Maechler <maechler@stat.math.ethz.ch>
2178 :    
2179 :     * R/AllGeneric.R (tcrossprod): 2-argument version; here, and for
2180 :     all methods (and help files).
2181 :    
2182 : maechler 1084 2005-12-09 Martin Maechler <maechler@stat.math.ethz.ch>
2183 :    
2184 :     * R/Auxiliaries.R (dimNamesCheck): fixed thinko -> bug
2185 :     for case (dimn. op no_dimn.)
2186 :    
2187 :     2005-11-14 Douglas Bates <bates@stat.wisc.edu>
2188 :    
2189 : maechler 1174 * DESCRIPTION (Version): 0.99-2 released to CRAN
2190 : maechler 1084
2191 : bates 988 2005-10-21 Douglas Bates <bates@stat.wisc.edu>
2192 :    
2193 :     * R/lmer.R (simulate method): Fixed a drop=FALSE problem reported
2194 :     by Julian Faraway.
2195 :    
2196 : maechler 976 2005-10-06 Martin Maechler <maechler@stat.math.ethz.ch>
2197 :    
2198 :     * R/Auxiliaries.R (try_as): new utility
2199 :     * R/sparseMatrix.R: use try_as() in coercion to original class
2200 :    
2201 : maechler 956 2005-09-30 Martin Maechler <maechler@stat.math.ethz.ch>
2202 :    
2203 :     * src/dgCMatrix.c (double_to_csc): and dgeMatrix_to_csc()
2204 :    
2205 :     2005-09-29 Martin Maechler <maechler@stat.math.ethz.ch>
2206 :    
2207 :     * R/Auxiliaries.R (dimNamesCheck): added
2208 :    
2209 :     * R/Matrix.R (as.array), (as.vector): new
2210 :    
2211 : maechler 954 2005-09-28 Martin Maechler <maechler@stat.math.ethz.ch>
2212 :    
2213 :     * R/Matrix.R (Matrix): get logical argument 'sparse' with a smart
2214 : maechler 956 default.
2215 :     * R/AllClass.R: move 'factors' slot toplevel "Matrix";
2216 :     "pMatrix" now contains "sparseMatrix"
2217 : maechler 954
2218 : maechler 948 2005-09-26 Martin Maechler <maechler@stat.math.ethz.ch>
2219 :    
2220 :     * tests/Class+Meth.R: new tests; t(t(m)) == m
2221 :    
2222 :     * src/dtCMatrix.c (tsc_transpose): add forgotten "diag" slot
2223 :    
2224 :     * src/dsTMatrix.c (dsTMatrix_as_dsCMatrix): bad typo (segfault!)
2225 :     * src/dtTMatrix.c (dtTMatrix_as_dtCMatrix): new
2226 :    
2227 :     * R/dspMatrix.R: typo in "t" method
2228 :    
2229 : maechler 925 2005-09-18 Douglas Bates <bates@wisc.edu>
2230 :    
2231 :     * R/AllClass.R (TsparseMatrix), CsparseM* and RsparseM*
2232 :     * R/Tsparse.R: instead of R/gTMatrix.R
2233 :     * R/Csparse.R: new
2234 :     * src/Tsparse.c (Tsparse_to_Csparse): new; -> cholmod_()
2235 :     * src/Tsparse.c: new; many trivial methods calling cholmod_()
2236 :     * src/Csparse.c (Csparse_to_Tsparse), transpose, (mat|cross)prod:
2237 :     via cholmod
2238 :    
2239 :     2005-09-16 Martin Maechler <maechler@stat.math.ethz.ch>
2240 :    
2241 :     * R/Auxiliaries.R (non0ind): new function using new C code
2242 :     * src/dgCMatrix.c (compressed_non_0_ij): new utility
2243 :    
2244 : bates 917 2005-09-15 Douglas Bates <bates@localhost.localdomain>
2245 :    
2246 :     * src/chm_common.h: header file required by all C sources that
2247 : maechler 1174 call CHOLMOD functions. It defines a cholmod_common structure
2248 : bates 917 called 'c' whose address is passed as the last argument to
2249 :     (virtually) every CHOLMOD function.
2250 :    
2251 :     * src/Pattern.c: Simple example of the use of CHOLMOD.
2252 :    
2253 :     * src/init.c: initialize and finalize the cholmod_common structure.
2254 :    
2255 :     * src/Makefile: Added source packages CHOLMOD UMFPACK AMD COLAMD
2256 :     LDL and CCOLAMD from the U. of Florida sparse matrix library.
2257 :    
2258 : maechler 908 2005-09-08 Martin Maechler <maechler@stat.math.ethz.ch>
2259 :    
2260 :     * inst/test-tools.R: new file collecting the utility functions used
2261 :     in ./tests/*.R
2262 :    
2263 :     * R/ddenseMatrix.R (cbind2): new methods for "numeric" and "matrix"
2264 :     * R/Matrix.R (cbind2): methods for NULL and missing
2265 :    
2266 : maechler 886 2005-08-31 Martin Maechler <maechler@stat.math.ethz.ch>
2267 :    
2268 :     * R/AllClass.R: new "index" class for "[" and "[<-":
2269 :     First cut at "symmetricMatrix" and "triangularMatrix"
2270 :     * R/gTMatrix.R (.ind.prep): new function;
2271 : maechler 1174 Logical and character indexing now work too.
2272 : maechler 886 * R/Matrix.R: cheap "[<-" methods for denseMatrix now work
2273 :     * tests/indexing.R: new, including *.Rout.save
2274 :     * tests/dgTMatrix.R: new
2275 :    
2276 : bates 876 2005-08-29 Douglas Bates <bates@wisc.edu>
2277 :    
2278 :     * src/dgTMatrix.c (graphNEL_as_dgTMatrix): Corrected the position
2279 :     indicator pos not being updated. Also enforced upper triangular
2280 :     for symmetric case. Need to coerce edges component of elements of
2281 :     edge list - grr! (Why don't they define their classes cleanly?)
2282 :    
2283 : maechler 871 2005-08-26 Martin Maechler <maechler@stat.math.ethz.ch>
2284 :    
2285 :     * R/Matrix.R: added first "[<-" methods; not yet functional
2286 : bates 1352 * R/denseMatrix.R: ditto
2287 : maechler 871 * man/Subassign-methods.Rd: new help file for these
2288 :    
2289 :     2005-08-25 Martin Maechler <maechler@stat.math.ethz.ch>
2290 :    
2291 :     * DESCRIPTION (Version): 0.98-6
2292 :    
2293 :     * R/denseMatrix.R: new file for "[" fallback methods for all dense
2294 :     matrices.
2295 :    
2296 : maechler 868 2005-08-19 Martin Maechler <maechler@stat.math.ethz.ch>
2297 :    
2298 :     * src/lgCMatrix.c (lcsc_to_matrix): new; need for
2299 :     as( <logical>, "matrix")
2300 :    
2301 :     * R/pMatrix.R: coercion to "lgTMatrix"
2302 :    
2303 :     * R/gTMatrix.R: new virtual class to define "[" methods for.
2304 :     * man/gTMatrix-class.Rd:
2305 :     * General slight re-organization of where "[" methods are defined.
2306 :     more to come.
2307 :    
2308 : maechler 871 2005-08-18 Douglas Bates <bates@wisc.edu>
2309 : maechler 868
2310 : maechler 1174 * DESCRIPTION (Version): 0.98-5 released to CRAN
2311 : maechler 871
2312 :     * src/dgTMatrix.c (graphNEL_as_dgTMatrix): add first graphNEL methods
2313 :     * .....
2314 :    
2315 : bates 863 2005-08-18 Douglas Bates <bates@localhost.localdomain>
2316 :    
2317 :     * R/lmer.R: Corrected naming scheme in mcmcsamp to work with lmer
2318 :     or glmer objects.
2319 :    
2320 : maechler 860 2005-08-17 Martin Maechler <maechler@stat.math.ethz.ch>
2321 :    
2322 :     * DESCRIPTION (Version): 0.98-4 : upload to CRAN
2323 :    
2324 :     2005-08-16 Douglas Bates <bates@localhost.localdomain>
2325 :    
2326 :     * R/HBMM.R: finish re-writing R-only code.
2327 :    
2328 : bates 854 2005-08-15 Douglas Bates <bates@localhost.localdomain>
2329 :    
2330 :     * man/externalFormats.Rd: move documentation for writeHB and
2331 :     writeMM here.
2332 :    
2333 :     * src/mmio.c: replace inclusion of <malloc.h> by <stdlib.h>
2334 :     (suggested by Paul Roecker).
2335 :    
2336 :     * tests/validObj.R (assertError): Comment out test that is failing
2337 :     after recent changes in r-devel.
2338 :    
2339 : maechler 860
2340 : maechler 848 2005-08-11 Martin Maechler <maechler@stat.math.ethz.ch>
2341 :    
2342 :     * R/AllClass.R: intermediate virtual class "denseMatrix"
2343 :     * man/denseMatrix-class.Rd
2344 :     * NAMESPACE: export it, and also export
2345 :     * man/unused-classes.Rd: "iMatrix", "zMatrix" and "ldenseMatrix"
2346 :    
2347 : bates 846 2005-08-10 Douglas Bates <bates@wisc.edu>
2348 :    
2349 : maechler 848 * DESCRIPTION (Version): 0.98-3 to CRAN
2350 :    
2351 : bates 846 * src/dtrMatrix.c (dtrMatrix_validate): fixed up validation and
2352 :     matrix_solve code (which was really, really wrong).
2353 :    
2354 : bates 835 2005-08-07 Douglas Bates <bates@wisc.edu>
2355 : maechler 834
2356 :     * DESCRIPTION (Version): 0.98-2
2357 :    
2358 :     * R/HBMM.R (readHB), (readMM): read Matrix Market formats
2359 :    
2360 :     * R/lmer.R (abbrvNms): new
2361 :     * R/lmer.R (mcmcsamp): allow transformed parameters
2362 : bates 835 * src/HBMM.c (Matrix_writeMatrixMarket): Added read/write routines
2363 :     for the Harwell-Boeing and the MatrixMarket formats.
2364 : maechler 834
2365 :     2005-08-04 Martin Maechler <maechler@stat.math.ethz.ch>
2366 :    
2367 :     * man/dtrMatrix-class.Rd: add examples
2368 : bates 835 * man/dtpMatrix-class.Rd: ditto; plus note about PROBLEM
2369 : maechler 834
2370 :     * TODO: note the dtpMatrix (docu) bug
2371 :    
2372 :     * R/zzz.R (.onLoad): assignInNamespace("as.matrix", *, "base")
2373 :     in order to ensure that new as.matrix() is used by old functions,
2374 :     e.g., svd(), qr(), eigen(), dist(),..;
2375 :     apply(), also matplot() or pairs().
2376 :    
2377 :    
2378 :     2005-08-03 Martin Maechler <maechler@stat.math.ethz.ch>
2379 :    
2380 :     * R/lmer.R: add 'fixme' comments and move the linear vs glm check;
2381 :     add comments about 'control' / lmerControl() arguments
2382 :    
2383 : bates 835 2005-07-27 Douglas Bates <bates@wisc.edu>
2384 : bates 820
2385 : bates 835 * man/sleepstudy.Rd: Added the sleep data set.
2386 : maechler 1174 * DESCRIPTION (Version): 0.98-1 released to CRAN
2387 : bates 820
2388 : bates 835 2005-07-12 Douglas Bates <bates@wisc.edu>
2389 : maechler 834 * man/sleepstudy.Rd: Added the sleep data set.
2390 :    
2391 : bates 809 * R/lmer.R (glmmMCMC): Added PACKAGE = "Matrix" in a couple of
2392 :     .Call calls that were producing spurious output.
2393 :    
2394 : bates 835 2005-07-05 Douglas Bates <bates@wisc.edu>
2395 : bates 801
2396 :     * R/lmer.R (lmer): stored updated variance component estimates in
2397 :     mer object for the generalized model. (Bug reported by Renaud
2398 :     Lancelot).
2399 :    
2400 : bates 835 2005-07-03 Douglas Bates <bates@wisc.edu>
2401 : bates 794
2402 :     * src/lmer.c (glmer_devAGQ): Added AGQ for single grouping factor,
2403 :     unidimensional case.
2404 :    
2405 : bates 835 2005-06-08 Douglas Bates <bates@wisc.edu>
2406 : maechler 791
2407 :     * DESCRIPTION (Version): 0.96-1
2408 :    
2409 : maechler 1174 * moved lmer-class' R and C code moved from lme4 to here
2410 : maechler 791
2411 : bates 835 2005-06-04 Douglas Bates <bates@wisc.edu>
2412 : bates 763
2413 :     * R/dgCMatrix.R: Call to csc_matrix_mm used undefined arguments
2414 :     (reported by Guissepe Ragusa <gragusa@ucsd.edu>)
2415 :    
2416 : bates 835 2005-06-02 Douglas Bates <bates@wisc.edu>
2417 : bates 763
2418 :     * src/Makefile.win: Forgot to update this when Makefile changed.
2419 :    
2420 : bates 835 2005-05-11 Douglas Bates <bates@wisc.edu>
2421 : bates 726
2422 :     * src/dgCMatrix.c (csc_transpose): Simplified function fixing a
2423 :     bug reported by Kurt Hornik and Michael Hahsler.
2424 :    
2425 : bates 835 2005-05-10 Douglas Bates <bates@wisc.edu>
2426 : bates 725
2427 :     * src/lgCMatrix.c (Matrix_lgClgCmm): Implementation of methods for
2428 :     logical sparse matrices. These will also be used in the symbolic
2429 :     analysis for lmer objects.
2430 :    
2431 :     * src/dsCMatrix.c (dsCMatrix_matrix_solve): Copied the dimensions
2432 :     of b to the result. Fixes bug reported by Jean.Coursol@math.u-psud.fr
2433 : maechler 791
2434 : bates 835 2005-05-06 Douglas Bates <bates@wisc.edu>
2435 : bates 714
2436 :     * src/dgeMatrix.c (dgeMatrix_colsums): Added an implementation of
2437 :     colMeans, colSums, rowMeans and rowSums.
2438 :    
2439 : bates 835 2005-04-18 Douglas Bates <bates@wisc.edu>
2440 : bates 692
2441 :     * src/lgCMatrix.[ch]: code for _validate method and stub for
2442 :     multiplication operation.
2443 :    
2444 :     * src/dgeMatrix.c (dgeMatrix_matrix_solve): Passing wrong argument
2445 :     to dgetrs.
2446 :    
2447 :     * src/init.c: Fix cut-and-paste error in definition of
2448 :     dgeMatrix_matrix_solve
2449 :    
2450 :     * src/{many files}: Tighten code by using ALLOC_SLOT.
2451 :    
2452 : bates 835 2005-04-15 Douglas Bates <bates@wisc.edu>
2453 : bates 692
2454 :     * R/AllClass.R: Add lgTMatrix and lgCMatrix classes
2455 :    
2456 :     * DESCRIPTION: Eliminate import of stats.
2457 :    
2458 : maechler 791
2459 : bates 835 2005-04-06 Douglas Bates <bates@wisc.edu>
2460 : bates 692
2461 :     * R/AllClass.R : add logical sparse matrix classes
2462 :    
2463 : maechler 687 2005-04-01 Martin Maechler <maechler@stat.math.ethz.ch>
2464 :    
2465 :     * R/dgTMatrix.R: add "[" method for triplet matrices
2466 :     * R/sparseMatrix.R: and other sparse ones; --> add show() for sparse
2467 :    
2468 : bates 835 2005-03-31 Douglas Bates <bates@wisc.edu>
2469 : maechler 687
2470 :     * DESCRIPTION (Version): release 0.95-5 to CRAN
2471 :    
2472 :     * R/dMatrix.R: add %*%, crossprod and solve "fallback" methods
2473 :     * R/sparseMatrix.R: %*%, crossprod()
2474 :     * R/dgeMatrix.R: more "fallback" methods for numeric/dense matrices
2475 :     * man/*.Rd: move method definitions to 'Matrix' and 'dMatrix'
2476 :     * src/lmer.c (lmer_fitted): fix thinko
2477 :    
2478 : maechler 676 2005-03-26 Martin Maechler <maechler@stat.math.ethz.ch>
2479 :    
2480 :     * R/AllClass.R: add two virtual sparse classes ``on top''
2481 :    
2482 :     2005-03-24 Martin Maechler <maechler@stat.math.ethz.ch>
2483 :    
2484 :     * R/AllClass.R (setClass): use "VIRTUAL" for the virtual classes;
2485 :     correspondingly fix examples and tests/ since new()
2486 :     doesn't work for virtual classes.
2487 :    
2488 : maechler 658 2005-03-17 Martin Maechler <maechler@stat.math.ethz.ch>
2489 :    
2490 :     * R/Matrix.R (as.matrix): method and one for unname()
2491 :     * tests/dpoMatrix.R: tests should now be less platform dependent;
2492 :     also run for R 2.1.0; using as.matrix()
2493 :    
2494 : bates 835 2005-03-15 Douglas Bates <bates@wisc.edu>
2495 : maechler 658
2496 :     * R/pMatrix.R: "pMatrix" class added
2497 :     * ....
2498 :    
2499 : bates 835 2005-03-14 Douglas Bates <bates@wisc.edu>
2500 : bates 645
2501 :     * R/dtpMatrix.R: Add unpack method and an example.
2502 :    
2503 :     * src/dsyMatrix.c (dsyMatrix_trf): Add BunchKaufman factorization
2504 :     of general symmetric matrices and associated S4 methods.
2505 :    
2506 : maechler 658 2005-03-10 Martin Maechler <maechler@stat.math.ethz.ch>
2507 :     +
2508 :     2005-03-05 Martin Maechler <maechler@stat.math.ethz.ch>
2509 :    
2510 :     * R/dgeMatrix.R (setAs): and many other files: more coercion,
2511 :     crossprod() and "%*%" methods added; tests, too.
2512 :     * tests/matprod.R: new, for testing these
2513 :    
2514 : bates 835 2005-03-03 Douglas Bates <bates@wisc.edu>
2515 : bates 599
2516 :     * src/lmer.c (lmer_fitted): Added.
2517 :    
2518 : bates 835 2005-03-02 Douglas Bates <bates@wisc.edu>
2519 : bates 596
2520 :     * R/dsTMatrix.R: Conversion from dsTMatrix to dsCMatrix
2521 :    
2522 : bates 835 2005-02-28 Douglas Bates <bates@wisc.edu>
2523 : bates 582
2524 :     * src/*.c,po/,inst/po: Internationalization and localization of
2525 :     the package.
2526 :    
2527 :     * src/ldl.[ch]: Removed these as their contents are referenced in the
2528 :     R_ldl.c file.
2529 :    
2530 :     * src/flame.[ch]: Removed these source files.
2531 : maechler 658
2532 : bates 582 * src/dtrMatrix.c (make_array_triangular): Move to Mutils
2533 :    
2534 :     * src/LU.[ch],src/init.c: absorb in factorizations
2535 :    
2536 :     * src/Mutils.h: prepare for internationalization
2537 :    
2538 :     * src/cblas.h: move the enum definitions to Mutils.h and remove
2539 :     this file
2540 :    
2541 : maechler 578 2005-02-26 Martin Maechler <maechler@stat.math.ethz.ch>
2542 :    
2543 : maechler 579 * R/dgeMatrix.R: provide "dimnames" and "dimnames<-" methods
2544 :    
2545 :     * R/dtrMatrix.R: fix t() method
2546 :    
2547 : maechler 578 * R/dgeMatrix.R: define group methods "Arith", "Math", "Math2"
2548 : maechler 658 * NAMESPACE: export them (and import generics from "methods")
2549 : maechler 578 * tests/group-methods.R : and test them.
2550 :    
2551 :     * src/dtrMatrix.c (dtrMatrix_as_dgeMatrix): prevent seg.fault in
2552 :     border case
2553 :    
2554 :     2005-02-24 Douglas Bates <bates@stat.wisc.edu>
2555 :    
2556 : maechler 658 * DESCRIPTION (Version): 0.95-2 released to CRAN
2557 : maechler 578
2558 :     * src/dgBCMatrix.c:
2559 :     * src/lmer.c: many changes
2560 :     * ...
2561 :    
2562 : maechler 512 2005-02-04 Martin Maechler <maechler@stat.math.ethz.ch>
2563 :    
2564 :     * R/Matrix.R: add more sophisticated show() method.
2565 :    
2566 : maechler 578 2005-02-02 Douglas Bates <bates@stat.wisc.edu>
2567 :    
2568 :     * */* : almost complete reorganization of classes.
2569 :    
2570 : bates 835 2005-01-26 Douglas Bates <bates@wisc.edu>
2571 : bates 460
2572 :     * R/AllGeneric.R: Added matrix exponential generic expm and a method
2573 :     for the geMatrix class.
2574 :    
2575 : bates 835 2005-01-24 Douglas Bates <bates@wisc.edu>
2576 : bates 460
2577 :     * src/Makefile (clean): Remove *.a and *.so
2578 :    
2579 :     * man/cscBlocked-class.Rd: Remove reference to the lmer-class.
2580 :    
2581 : bates 835 2005-01-23 Douglas Bates <bates@wisc.edu>
2582 : bates 460
2583 : maechler 658 * src/lmer.c (Lind): Definition of Lind was backwards. This only
2584 : bates 460 had an effect in cases with more than 2 grouping factors.
2585 :    
2586 : bates 835 2005-01-03 Douglas Bates <bates@wisc.edu>
2587 : bates 415
2588 :     * src/lmeRep.c (lmer_variances): change from lmeRep to lmer
2589 :    
2590 : bates 835 2004-12-23 Douglas Bates <bates@wisc.edu>
2591 : bates 410
2592 :     * src/init.c (R_init_Matrix): Reorder calls to R_registerRoutines
2593 :     and R_useDynamicSymbols (suggested by B.D.Ripley).
2594 :    
2595 : bates 835 2004-12-14 Douglas Bates <bates@wisc.edu>
2596 : bates 392
2597 :     * R/sscMatrix.R: Add determinant methods
2598 :    
2599 :     * src/triplet.[ch],src/init.c (triplet_to_matrix): Add a coercion
2600 :     for tripletMatrix to matrix.
2601 :    
2602 : bates 835 2004-12-13 Douglas Bates <bates@wisc.edu>
2603 : bates 388
2604 : bates 392 * R/AllClass.R (.onLoad): Eliminate the bbCrosstab class, which is
2605 :     no longer used.
2606 :    
2607 : bates 388 * src/R_ldl.c: Created an R-specific version of the ldl.[ch] files
2608 :     with dynamic allocation of scratch arrays.
2609 :    
2610 :     * src/ssclme.c (ssclme_copy_ctab): Fixed bug in creation of ZtZ
2611 :     for multivariate random effects with multiple grouping factors.
2612 :     Fixes part but not all of #15.
2613 :    
2614 : bates 835 2004-12-03 Douglas Bates <bates@wisc.edu>
2615 : bates 375
2616 :     * src/lmeRep.c (lmeRep_factor): order of operations for multiple
2617 :     scalar grouping factors corrected.
2618 :    
2619 : bates 835 2004-11-29 Douglas Bates <bates@wisc.edu>
2620 : bates 375
2621 :     * src/bCrosstab.c: remove diag_update which is no longer used
2622 :    
2623 : bates 835 2004-11-16 Douglas Bates <bates@wisc.edu>
2624 : bates 350
2625 :     * src/Metis_utils.c: Move metis.h include to C sources so that the
2626 :     .h file can be included.
2627 :    
2628 : bates 835 2004-11-12 Douglas Bates <bates@wisc.edu>
2629 : bates 342
2630 : bates 350 * src/LU.c,geMatrix.c,trMatrix.c, etc.:
2631 : bates 342 Complete allocation of slots in NEW_OBJECT.
2632 :    
2633 :     * src/Mutils.h: Moved list of symbols to an include file
2634 :    
2635 : bates 835 2004-11-11 Douglas Bates <bates@wisc.edu>
2636 : bates 342
2637 :     * src/geMutils.c (Matrix_init): remove unused function
2638 :    
2639 : bates 835 2004-11-10 Douglas Bates <bates@wisc.edu>
2640 : bates 342
2641 :     * src/cscMatrix.c (csc_to_imagemat): removed unused function
2642 :    
2643 : bates 835 2004-11-05 Douglas Bates <bates@wisc.edu>
2644 : bates 327
2645 :     * src/Makefile.win (SOURCES_C): Keep consistent with Makefile
2646 :    
2647 : bates 835 2004-10-27 Douglas Bates <bates@wisc.edu>
2648 : bates 303
2649 :     * R/pdmatrix.R: remove PACKAGE="Matrix" in .Call calls
2650 :    
2651 : bates 835 2004-10-04 Douglas Bates <bates@wisc.edu>
2652 : bates 296
2653 :     * src/init.c: Created R_init_Matrix and added registration of C
2654 :     routines.
2655 :    
2656 : bates 835 2004-10-02 Douglas Bates <bates@wisc.edu>
2657 : bates 283
2658 :     * R/tripletMatrix.R: Force a require(lattice) for the image methods.
2659 :    
2660 : bates 835 2004-06-15 Douglas Bates <bates@wisc.edu>
2661 : bates 229
2662 :     * man/trMatrix-class.Rd: Escape the % chars in .Rd files.
2663 :    
2664 : bates 111 2004-04-20 Douglas Bates <bates@stat.wisc.edu>
2665 :    
2666 :     * src/Makefile.win ($(SHLIB)): Modifications per Uwe Ligges.
2667 :    
2668 : bates 109 2004-04-19 Douglas Bates <bates@stat.wisc.edu>
2669 :    
2670 :     * src/ssclme.c (ssclme_update_mm): fix logic error in
2671 :     ssclme_update_mm
2672 :    
2673 : bates 105 2004-04-18 Douglas Bates <bates@stat.wisc.edu>
2674 :    
2675 :     * src/ssclme.c (ssclme_coef, ssclme_coefGets): Create consistency
2676 :     in the order of unconstrained and constrained parameters.
2677 :     (ssclme_gradient): Added the gradients (not yet correct for
2678 :     multidimensional, unconstrained case).
2679 :    
2680 : bates 78 2004-04-14 Douglas Bates <bates@stat.wisc.edu>
2681 :    
2682 :     * src/ssclme.c (ssclme_EMsteps): Fix logic in REML update
2683 :    
2684 :     * src/Makefile.win: Remove unneeded ranlib call
2685 :    
2686 : bates 71 2004-04-12 Douglas Bates <bates@stat.wisc.edu>
2687 :    
2688 :     * DESCRIPTION (Version): New release
2689 :    
2690 :     * src/Makefile.win: Update Makefile.win to umfpack removal.
2691 :    
2692 : bates 49 2004-04-05 Douglas Bates <bates@bates2_home>
2693 :    
2694 :     * src/triplet_to_col.c: Create triplet_to_col as a native
2695 : maechler 658 function, not the version from umfpack. There were problems with
2696 : bates 49 the configuration of UMFPACK for 64-bit processors and there was
2697 :     only one umfpack routine being used so I moved it here.
2698 :    
2699 : bates 45 2004-04-04 Douglas Bates <bates@bates2_home>
2700 :    
2701 :     * src/ssclme.c (ssclme_variances): New function.
2702 :    
2703 : bates 28 2004-03-28 Douglas Bates <bates@bates2_home>
2704 :    
2705 :     * src/ssclme.c (ssclme_fitted): Added function.
2706 :    
2707 : bates 22 2004-03-27 Douglas Bates <bates@bates2_home>
2708 :    
2709 :     * src/ssclme.c (ssclme_transfer_dimnames): Add new function to
2710 :     store the dimnames in the XtX and bVar slots
2711 :     (ssclme_update_mm): Change the dimensions of the bVar slot
2712 :     components and the returned value from ssclme_ranef.
2713 :    
2714 : bates 10 2004-03-18 Douglas Bates <bates@stat.wisc.edu>
2715 :    
2716 :     * R/{pdMat.R,pdIdent.R,pdLogChol.R,pdMatrixLog.R,pdNatural.R},
2717 :     src/{pdMat.c,pdIdent.c,pdLogChol.c,pdNatural.c},
2718 :     tests/{pdCompSymm.R,pdDiag.R,pdIdent.R,pdLogChol.R,pdNatural.R},
2719 :     man/{pdMat-class.Rd,pdmatrix-class.Rd,corrmatrix-class.Rd,
2720 :     pdDiag-class.Rd,pdIdent-class.Rd,pdNatural-class.Rd,
2721 :     pdLogChol-class.Rd,coefGets.Rd,pdCompSymm-class.Rd,
2722 :     pdfactor-class.Rd,pdFactor.Rd,pdMatrix.Rd,
2723 :     pdBlocked-class.Rd},AllClass.R,AllGeneric.R:
2724 :     Moved the pdMat classes from the lme4 package.
2725 :    
2726 :     2004-03-02 Douglas Bates <bates@stat.wisc.edu>
2727 :    
2728 :     * man/ssclme-class.Rd: Update definition and documentation of the
2729 :     ssclme class to include the DIsqrt slot.
2730 :    
2731 :     * src/ssclme.c (ssclme_deviance): Modify order of computation
2732 :     (much faster using dsyrk, a level 3 BLAS routine).
2733 :    
2734 :     * src/Makefile (SUBLIBS): Change definition (K. Hornik)
2735 :    
2736 :     2004-02-28 Douglas Bates <bates@stat.wisc.edu>
2737 :    
2738 :     * tests/ssclme.R: Modify the test to account for the permutation
2739 :     of the levels of the grouping factors.
2740 :    
2741 :     2004-02-23 Douglas Bates <bates@stat.wisc.edu>
2742 :    
2743 :     * R/ssclme.R,src/ssclme.c (ssclme): Move slots of sscCrosstab slot
2744 :     directly into the ssclme class definition.
2745 :    
2746 :     2004-02-22 Douglas Bates <bates@stat.wisc.edu>
2747 :    
2748 :     * DESCRIPTION (Date): New release
2749 :    
2750 :     * man/ssclme-class.Rd: new file.
2751 :    
2752 :     * src/ssclme.c (ssclme_loglik): major revisions in design. It
2753 :     works and it's fast!
2754 :    
2755 :     2004-02-17 Douglas Bates <bates@stat.wisc.edu>
2756 :    
2757 :     * src/taucs/Makefile.win (lib): Change "ar" to "$(AR)" (B.Ripley)
2758 :    
2759 :     2004-02-16 Douglas Bates <bates@stat.wisc.edu>
2760 :    
2761 :     * DESCRIPTION (Date): New release
2762 :    
2763 :     * NAMESPACE: Don't export ssclme.
2764 :    
2765 :     * data/ScotsSec.rda, man/ScotsSec.Rd: Add Scottish secondary
2766 :     school data.
2767 :    
2768 :     2004-02-11 Douglas Bates <bates@stat.wisc.edu>
2769 :    
2770 :     * src/sscCrosstab.c (sscCrosstab): Added a row to the incidence to
2771 :     keep track of the fixed-effects and the response. Counts also
2772 :     gets an extra element, which is always one.
2773 :    
2774 :     * src/ldl.c: Include these routines from Tim Davis' LDL package.
2775 :    
2776 :     2004-02-10 Douglas Bates <bates@stat.wisc.edu>
2777 :    
2778 :     * src/cscMatrix.c (csc_transpose): new function
2779 :    
2780 :     * src/Mutils.c (csc_sort_columns): perm/iperm confusion corrected
2781 :     (csc_components_transpose): new function
2782 :    
2783 :     2004-02-06 Douglas Bates <bates@stat.wisc.edu>
2784 :    
2785 :     * src/triplet.c (triplet_validate): Fix Dim slot on generated
2786 :     triplets
2787 :    
2788 :     2004-01-30 Douglas Bates <bates@stat.wisc.edu>
2789 :    
2790 :     * R/sscCrosstab.R (sscCrosstab): Added sscCrosstab generator function.
2791 :    
2792 :     * src/LU.h (MATRIX_LU_H): Add #ifndef #define ... #endif to this
2793 :     and all other .h files in src.
2794 :    
2795 :     * src/Makefile.win: This and other Makefile.win files contributed
2796 :     by Brian Ripley.
2797 :    
2798 :     2004-01-27 Douglas Bates <bates@stat.wisc.edu>
2799 :    
2800 :     * R/syMatrix.R: Added methods for "%*%".
2801 :    
2802 :     * R/Hilbert.R (Hilbert): Changed Hilbert function to return a
2803 :     poMatrix object.
2804 :    
2805 :     2004-01-26 Douglas Bates <bates@stat.wisc.edu>
2806 :    
2807 :     * man/sscChol-class.Rd,man/mm.Rd,man/y.Rd: Added man pages.
2808 :    
2809 :     2004-01-25 Douglas Bates <bates@bates2_home>
2810 :    
2811 :     * inst/doc/Introduction.Rnw,Comparisons.Rnw: Added vignettes.
2812 :    
2813 :     * R/csc.R: Convert all cscMatrix classes to use Dim slot instead
2814 :     of nrow.
2815 :    
2816 :     2003-12-31 Douglas Bates <bates@stat.wisc.edu>
2817 :    
2818 :     * src/taucs/taucs.h: Moved taucs.h, amd.h, and umfpack.h into
2819 :     subdirectories.
2820 :    
2821 :     2003-12-08 Douglas Bates <bates@stat.wisc.edu>
2822 :    
2823 :     * src/taucs.h: Accidently referred to global header files
2824 :     instead of local files.
2825 :    
2826 :     2003-12-04 Douglas Bates <bates@stat.wisc.edu>
2827 :    
2828 :     * R/AllClass.R: Lots of changes. Removed all the lapack++ code
2829 :     and methods and replaced all classes with S4 classes.
2830 :    
2831 :     2003-04-19 Douglas Bates <bates@stat.wisc.edu>
2832 :    
2833 :     * R/det.R,man/det.Rd: Change name of det generic to determinant
2834 :    
2835 :     * src/R_LapackPP.cc: Change method of calculating determinants
2836 :    
2837 :     2003-02-03 Douglas Bates <bates@stat.wisc.edu>
2838 :    
2839 :     * DESCRIPTION (Version): removed empty data directory as requested
2840 :     by CRAN maintainers. Changed version number and date.
2841 :    
2842 :     2002-10-23 Douglas Bates <bates@stat.wisc.edu>
2843 :    
2844 :     * src/laindex.h: Applied patches from Brian Ripley for compilation
2845 :     under Windows.
2846 :    
2847 :     * Added configure.win and src/Makevars.win as requested by Brian
2848 :     Ripley.
2849 :    
2850 :     2002-05-03 Douglas Bates <bates@stat.wisc.edu>
2851 :    
2852 :     * src/lamatrix.h: Removing pre-1.2.0 compatibility code per Kurt
2853 :     Hornik.
2854 :    
2855 :     2002-04-24 Douglas Bates <bates@stat.wisc.edu>
2856 :    
2857 :     * configure.ac: Replaced configure.in with configure.ac
2858 :     contributed by Kurt Hornik.
2859 :    
2860 :     * aclocal.m4 (ac_clean_files): Replaced this with Kurt Hornik's
2861 :     version for R-1.5.0
2862 :    
2863 : maechler 512
2864 : bates 10 2001-12-10 Douglas Bates <bates@stat.wisc.edu>
2865 :    
2866 :     * man/eigen.Rd: Removed the .Alias in the example

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