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Annotation of /pkg/ChangeLog

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1 : mmaechler 2206 2008-06-25 Martin Maechler <maechler@stat.math.ethz.ch>
2 :    
3 :     * R/diagMatrix.R (.bdiag): use more efficient Bates-algorithm for
4 :     .bdiag().
5 :     * man/bdiag.Rd: update, including test.
6 :    
7 :     2008-06-24 Martin Maechler <maechler@stat.math.ethz.ch>
8 :    
9 :     * tests/Simple.R: add minimal bdiag() checks
10 :    
11 :     * R/diagMatrix.R (bdiag): fix bdiag(diag(4:5)) case;
12 :     factor out the Tsparse - internal computation into new .bdiag()
13 :    
14 : mmaechler 2203 2008-06-14 Martin Maechler <maechler@stat.math.ethz.ch>
15 :    
16 :     * R/nsparseMatrix.R: specific fast all() and any() methods.
17 :    
18 :     * src/dgTMatrix.c (MAKE_gTMatrix_to_geMatrix): better error message
19 :     when trying to produce too large result.
20 :    
21 :     * inst/test-tools.R (checkMatrix): add 'do.matrix' with a check for
22 :     very large matrices.
23 :    
24 :     * R/sparseMatrix.R (printSpMatrix2): new function, used by
25 :     show(<sparseMatrix>).
26 :    
27 :     * R/diagMatrix.R (show): print only diagonal entries when nrow(.) >= 50.
28 :    
29 :     2008-06-13 Martin Maechler <maechler@stat.math.ethz.ch>
30 :    
31 :     * src/Mutils.c (m_encodeInd, m_encodeInd2):
32 :     * R/*.R: .Call(m_encodeInd2?, ..) instead of encodeInd2?(..).
33 :    
34 :     * R/Auxiliaries.R (encodeInd2?): care against integer overflow (for
35 :     big matrices): -> 2nd argument 'di' instead of 'nr' !
36 :    
37 : mmaechler 2202 2008-06-09 Martin Maechler <maechler@stat.math.ethz.ch>
38 :    
39 :     * R/dtCMatrix.R: faster dgC* -> dtC* method
40 :     * tests/Simple.R: (hence removed "FIXME")
41 :    
42 :     * R/Auxiliaries.R (copyClass): add 'check = .copyClass.check'
43 :     which can be be turned off for possible speed gains.
44 :    
45 : mmaechler 2199 2008-06-02 Martin Maechler <maechler@stat.math.ethz.ch>
46 :    
47 :     * R/dMatrix.R, R/Tsparse.R: get rid of some disambiguation warnings
48 :    
49 :     * R/not.R: fix !<ldiMatrix>
50 :     implement two old "FIXME"s: !<ldenseMatrix> & !<ndenseMatrix>
51 :    
52 :     * R/diagMatrix.R (Ops): fix one-off thinko in
53 :     <diagonal> o <numeric> methods
54 :    
55 :     * inst/test-tools.R: checkMatrix(): drop0(m12) unconditionally
56 :    
57 : mmaechler 2196 2008-05-30 Martin Maechler <maechler@stat.math.ethz.ch>
58 :    
59 :     * R/diagMatrix.R (Ops): more <diagonal> o <Matrix> methods
60 :     * tests/Simple.R: testing the above
61 :    
62 : mmaechler 2194 2008-05-07 Martin Maechler <maechler@stat.math.ethz.ch>
63 :    
64 :     * NAMESPACE: also import "Ops" {found via new tools:::get_S4_generics_with_methods()}
65 :    
66 : mmaechler 2193 2008-05-03 Martin Maechler <maechler@stat.math.ethz.ch>
67 :    
68 :     * R/Matrix.R (dimnames<-): dimnames(.) <- NULL works with a message;
69 :     * NAMESPACE (unname): finally exported
70 :    
71 : mmaechler 2186 2008-04-28 Martin Maechler <maechler@stat.math.ethz.ch>
72 :    
73 : mmaechler 2190 * R/Auxiliaries.R (cholMat): possibly keep packed
74 :    
75 : mmaechler 2188 * inst/test-tools.R (checkMatrix): add fixed determinant.matrix()
76 :     for R < 2.7.0.
77 :    
78 : mmaechler 2186 * R/Tsparse.R ([): for triangularMatrix, check if result may be
79 :     triangular.
80 :     * tests/indexing.R: regression test
81 :    
82 : mmaechler 2185 2008-04-26 Martin Maechler <maechler@stat.math.ethz.ch>
83 :    
84 :     * inst/test-tools.R (checkMatrix): test <Ops> not only for dMatrix
85 :     * R/Ops.R: more methods, for lMatrix/nMatrix
86 :    
87 : mmaechler 2183 2008-04-24 Martin Maechler <maechler@stat.math.ethz.ch>
88 :    
89 :     * R/expm.R: new file for all expm() methods; notably new ones for
90 :     diagonal*, triangular*, symmetric* and also simple "matrix".
91 :    
92 : mmaechler 2175 2008-04-23 Martin Maechler <maechler@stat.math.ethz.ch>
93 :    
94 : mmaechler 2183 * R/dsyMatrix.R: setAs(.) rather than setIs(.) "to dpoMatrix"
95 :    
96 :     * inst/test-tools.R (assert.EQ.mat): better message when not equal
97 :    
98 :     * src/dgeMatrix.c (dgeMatrix_matrix_crossprod): allow integer RHS.
99 :    
100 :     * R/AllClass.R (ddiMatrix,ldiMatrix): extend [dl]Matrix instead of
101 :     [dl]denseMatrix {identical slots; but more logical method dispatch}
102 :    
103 :     2008-04-23 Martin Maechler <maechler@stat.math.ethz.ch>
104 :    
105 : mmaechler 2175 * R/sparseMatrix.R (summary): use length(<i-slot>) instead of nnzero()
106 :    
107 :     * R/diagMatrix.R (determinant): method
108 :    
109 :     2008-04-22 Martin Maechler <maechler@stat.math.ethz.ch>
110 :    
111 :     * src/dsCMatrix.c (dsCMatrix_Cholesky): suppress CHOLMOD printing too
112 :    
113 :     * R/Rsparse.R (.viaC.to.R): uplo fix for symmetric & triangular
114 :    
115 :     * R/dsCMatrix.R (determinant): switch to use Cholesky( 'LDL' ) and
116 :     its diagonal
117 :    
118 :     2008-04-21 Martin Maechler <maechler@stat.math.ethz.ch>
119 :    
120 :     * R/dMatrix.R (Summary): short-cut for prod(<sparse>)
121 :    
122 :     * R/not.R: fix !<"U"-diag-ltrMatrix> ; drop {R < 2.6.0}-branch
123 :    
124 :     * R/Auxiliaries.R (tT2gT): fix for "U"-diag-ltTMatrix
125 :    
126 :     * R/AllClass.R: ltTMatrix validity: call (more stringent) tTMatrix_validate
127 :    
128 :     2008-04-19 Martin Maechler <maechler@stat.math.ethz.ch>
129 :    
130 :     * R/Ops.R (Ops.x.x): aux.function, not just for (dMatrix,dMatrix)
131 :    
132 :     * R/Ops.R (.do.Logic.lsparse): fix NA case
133 :    
134 :     * R/Tsparse.R (replTmat): fix r.sym case, using indTri()
135 :    
136 :     * R/Auxiliaries.R (nnzero): fix special cases, using
137 :     * R/Auxiliaries.R (indDiag): new utility
138 :     * R/Auxiliaries.R (indTri): new argument 'diag'
139 :    
140 :     * R/dMatrix.R: Summmary(<ddenseMatrix>): different branch for dsy*
141 :    
142 :     2008-04-18 Martin Maechler <maechler@stat.math.ethz.ch>
143 :    
144 :     * R/diagMatrix.R: "Summary" methods, and more "Arith" / "Ops"
145 :    
146 :     * src/Csparse.c (Csparse_drop): preserve (uplo,diag) for
147 :     ".tCMatrix" triangular matrix.
148 :    
149 :     * R/Auxiliaries.R (drop0): use diagU2N(); according to helpfile,
150 :     'clx' can be class *or* class representation.
151 :     (nnzSparse): new.
152 :     (non0ind): new 'xtendSymm' argument; used in
153 :     * R/Ops.R:
154 :    
155 :     * R/pMatrix.R: more efficient determinant() method
156 :    
157 :     2008-04-17 Martin Maechler <maechler@stat.math.ethz.ch>
158 :    
159 :     * [disactivated] R/Matrix.R (det): det() as base::det(), but with Matrix environment
160 :     * [disactivated] NAMESPACE: export(det)
161 :    
162 :     * R/diagMatrix.R (mkDiag): new substitute for diag()
163 :    
164 :     * R/Auxiliaries.R (nnzero): fix for "diagU2N"-case
165 :     (as0, as1): new utility.
166 :    
167 :     * R/Csparse.R (diag, band): need diagU2N()
168 :    
169 :     * src/dgeMatrix.c (get_norm): return NA when 'x' slot has NA/NaN.
170 :    
171 :     * R/lMatrix.R: coerce(nMatrix |-> lMatrix) fix
172 :    
173 :     * R/Ops.R (Compare): fix <nsp> o <nsp> case
174 :    
175 :     * R/nsparseMatrix.R, R/pMatrix.R: is.na() method
176 :    
177 :     2008-04-16 Martin Maechler <maechler@stat.math.ethz.ch>
178 :    
179 :     * R/Auxiliaries.R (signPerm): new utility for
180 :     * R/Auxiliaries.R (detSparseLU): determinant() via sparseLU
181 :    
182 :     * src/dsCMatrix.c (dsCMatrix_LDL_D): suppress 'CHOLMOD warning';
183 :     since we have our own error handler (and can use tryCatch() from R).
184 :    
185 :     2008-04-15 Martin Maechler <maechler@stat.math.ethz.ch>
186 :    
187 :     * R/dgTMatrix.R (image): ha! set col=NA if lwd is small -- very nice!
188 :    
189 :     * R/dsCMatrix.R (determinant): use tryCatch() and switch to lu()
190 :     when not positive definite.
191 :    
192 :     * R/Auxiliaries.R (asTri): new auxiliary
193 :     (non0.i): make *much* faster for Tsparse with many non-zero
194 :     entries; add 'uniqT = TRUE' argument to be used when sorting is undesired.
195 :    
196 :     * tests/Class+Meth.R (dotestMat): now build on checkMatrix() from
197 :     test-tools.R , see below
198 :    
199 :     * R/dMatrix.R: fix "Summary" method: + diagU2N()
200 :    
201 :     * NAMESPACE, R/Matrix.R: add mean() method
202 :    
203 :     2008-04-12 Martin Maechler <maechler@stat.math.ethz.ch>
204 :    
205 :     * R/dgTMatrix.R (image): allow to *not* take abs(), and use
206 :     cold-hot colors; try *changed* default useAbs = FALSE
207 :     * man/image-methods.Rd: nice examples
208 :    
209 :     2008-04-11 Martin Maechler <maechler@stat.math.ethz.ch>
210 :    
211 :     * inst/test-tools.R (checkMatrix): new function for modularizing part
212 :     of tstMatrixClass() in tests/Class+Meth.R
213 :    
214 :     * R/dsCMatrix.R: coercion from "matrix"
215 :     * R/ltTMatrix.R, R/ntTMatrix.R: ditto (change it).
216 :    
217 :     * tests/Class+Meth.R (tstMatrixClass): some cleanup;
218 :     add test for as(matrix(,0,0), <class>)
219 :    
220 :     2008-04-09 Martin Maechler <maechler@stat.math.ethz.ch>
221 :    
222 :     * src/dgeMatrix.c (dgeMatrix_determinant): for n == 0,
223 :     work as determinant(matrix(,0,0)).
224 :    
225 :     * src/dgCMatrix.c (dgCMatrix_LU): return {L,U} as dtCMatrix
226 :     * man/sparseLU-class.Rd: ditto
227 :    
228 :     * R/dgCMatrix.R (determinant): method building on lu()
229 :     * R/sparseMatrix.R, Matrix.R, ...: ditto
230 :    
231 :     * R/Auxiliaries.R (mkDet): auxiliary for determinant()
232 :    
233 :     2008-04-07 Martin Maechler <maechler@stat.math.ethz.ch>
234 :    
235 :     * R/sparseMatrix.R (summary<sparseMatrix>): no 'x' column for
236 :     pattern matrices.
237 :    
238 : maechler 2166 2008-04-02 Martin Maechler <maechler@stat.math.ethz.ch>
239 :    
240 :     * src/dense.c (dense_to_Csparse): all declarations *before*
241 :     R_CheckStack(); needed e.g. for ancient gcc 2.96.
242 :    
243 :    
244 : maechler 2159 2008-03-29 Martin Maechler <maechler@stat.math.ethz.ch>
245 :    
246 :     * DESCRIPTION (Version): 0.999375-9 --- need to release
247 :     for R-devel (and R 2.7.0 alpha soon).
248 :    
249 : maechler 2165 * R/AllClass.R: drop "double" from "atomicVector" class union
250 :    
251 : maechler 2161 * R/AllGeneric.R (rcond): check for base::rcond instead of R version
252 : maechler 2164 * R/dgeMatrix.R: ditto
253 : maechler 2161
254 : maechler 2159 * R/sparseMatrix.R (summary): count NAs
255 :    
256 : maechler 2165 * inst/doc/Intro2Matrix.Rnw: changes, aim for *one* introduction.
257 :    
258 : maechler 2158 2008-03-28 Martin Maechler <maechler@stat.math.ethz.ch>
259 :    
260 :     * R/AllGeneric.R: rcond(., norm) instead of rcond(., type), in
261 :     order to become compatible to new R 2.7.0 base::rcond().
262 :    
263 : maechler 2157 2008-03-25 Martin Maechler <maechler@stat.math.ethz.ch>
264 :    
265 : maechler 2158 * DESCRIPTION (Version,Date): 0.999375-8 --- released to CRAN
266 : maechler 2157
267 :     * R/diagMatrix.R (Ops): fix newly introduce bug in <.di> o <numeric>
268 :    
269 :     * inst/test-tools.R (isValid): new utility, used much in
270 :     * tests/simple.R:
271 :    
272 :     * man/BunchKaufman-methods.Rd: added too
273 :    
274 :     2008-03-24 Martin Maechler <maechler@stat.math.ethz.ch>
275 :    
276 :     * R/dsyMatrix.R: add BunchKaufman() methods.
277 :     * R/dspMatrix.R:
278 :    
279 :     * src/init.c: add dsyMatrix_trf
280 :    
281 :     2008-03-23 Douglas Bates <bates@stat.wisc.edu>
282 :    
283 :     * DESCRIPTION (Version): release 0.999375-7
284 :     * src/CHMfactor.c (CHMfactor_update): fix
285 :    
286 : maechler 2154 2008-03-22 Martin Maechler <maechler@stat.math.ethz.ch>
287 :    
288 :     * src/dsCMatrix.c (dsCMatrix_LDL_D): cleanup, also using
289 :     internal_chm_factor().
290 :    
291 :     * R/AllGeneric.R: do *not* define a "chol" generic
292 :     (but rather use the implicit one *without* making pivot
293 :     part of the signature)
294 :     * R/*.R: drop the 'pivot' from chol's signature and make
295 :     'pivot=FALSE' a default argument of method definitions.
296 :    
297 :     * .Rbuildignore: add 'wrld_1deg': I.e. do not put it into released
298 :     version of Matrix
299 :    
300 : maechler 2139 2008-03-18 Martin Maechler <maechler@stat.math.ethz.ch>
301 :    
302 : maechler 2144 * R/Tsparse.R (.T.2.n): drop 0's before coercion to "nMatrix"
303 :    
304 :     * R/sparseMatrix.R (is.na): new simple method
305 :     * R/denseMatrix.R (is.na): ditto.
306 :    
307 :     * R/diagMatrix.R (.symDiagonal): newly exported utility.
308 :    
309 :     * R/diagMatrix.R (Ops): <diag> * <numeric> should not become dgeMatrix!
310 :    
311 : maechler 2139 * src/UFsparse_download.sh: -->
312 :     * src/CHOLMOD/: update to CHOLMOD version 1.6 (Nov.2007)
313 :    
314 : maechler 2137 2008-03-17 Martin Maechler <maechler@stat.math.ethz.ch>
315 :    
316 :     * src/dsCMatrix.c (dsCMatrix_LDL_D): even faster utility with same
317 :     functionality; barely tested in
318 :     * tests/factorizing.R
319 :    
320 :     * src/Csparse.c (diag_tC): new functionality to enable faster
321 :     determinant(<dsCMatrix>, .) in
322 :     * R/dsCMatrix.R
323 :    
324 :     2008-03-17 18:53 Douglas Bates <bates@stat.wisc.edu>
325 :    
326 :     * R/CHMfactor.R, inst/include/Matrix.h, inst/include/Matrix_stubs.c,
327 :     src/CHMfactor.c, src/CHMfactor.h,
328 :     man/CHMfactor-class.Rd, src/init.c, tests/factorizing.R:
329 :     Log-determinant of the parent matrix from a CHMfactor object as
330 :     chm_factor_ldetL2; documentation and support
331 :    
332 :     2008-03-15 Martin Maechler <maechler@stat.math.ethz.ch>
333 :    
334 :     * R/dsCMatrix.R: enable determinant(<dsCMatrix>, .) via chol(.)
335 :    
336 : maechler 2130 2008-03-14 Martin Maechler <maechler@stat.math.ethz.ch>
337 :    
338 :     * R/dsCMatrix.R: setAs(., "dsCMatrix") but with a deprecation
339 :     warning.
340 :    
341 : maechler 2128 2008-03-13 Martin Maechler <maechler@stat.math.ethz.ch>
342 :    
343 :     * DESCRIPTION (Version, Date): bug-fix release 0.999375-6
344 :    
345 :     * R/diagMatrix.R (diag2tT.u): utility to be smarter in
346 :     <diagonal> o <sparse_triangular>
347 :     setAs(., "nMatrix") added.
348 :    
349 :     * R/diagMatrix.R (Diagonal): Diagonal(4, x=3) now works too
350 :    
351 :     * R/Auxiliaries.R (.diagU2N): more careful coercion in 2 steps
352 :     new argument 'checkDense = FALSE'.
353 :    
354 :    
355 : maechler 2125 2008-03-07 Martin Maechler <maechler@stat.math.ethz.ch>
356 :    
357 : maechler 2127 * src/dgeMatrix.c (dgeMatrix_exp): fix the octave-origin bug in the
358 :     back-permutation of the matrix exponential.
359 :    
360 :     * tests/matr-exp.R: test the fix (for an example where expm() was wrong).
361 :    
362 : maechler 2126 * DESCRIPTION (Date,Version): ready to release 0.999375-5
363 :    
364 : maechler 2125 * tests/simple.R: testing diagN2U
365 :    
366 :     2008-03-06 Martin Maechler <maechler@stat.math.ethz.ch>
367 :    
368 :     * R/Auxiliaries.R (diagN2U): interface to
369 :    
370 :     * src/Csparse.c (Csparse_diagN2U): .Call()able SEXP version of chm_diagN2U()
371 :    
372 :     * tests/matprod.R: test for triangularity preserving <dtC> %*% <dtC>
373 :    
374 : maechler 2123 2008-03-05 Martin Maechler <maechler@stat.math.ethz.ch>
375 :    
376 : maechler 2125 * src/chm_common.c (chm_diagN2U): new utility.
377 :    
378 :     * src/Csparse.c (Csparse_Csparse_crossprod, Csparse_Csparse_prod):
379 :     make use of chm_diagN2U() and hence now preserve triangularity and
380 :     unit-triangularity.
381 :    
382 : maechler 2123 * DESCRIPTION (LicenseDetails): new; such that 'License:' becomes "canonical"
383 :    
384 : maechler 2120 2008-03-04 Martin Maechler <maechler@stat.math.ethz.ch>
385 :    
386 :     * R/diagMatrix.R (subDiag): fix when x[..] became a vector
387 :    
388 :     * src/Tsparse.c (Tsparse_diagU2N): new utility, necessary for e.g.
389 :     * src/Csparse.c (Csparse_crossprod): use [CT]sparse_diagU2N() !!
390 :    
391 :     * R/Auxiliaries.R (.diagU2N): make use of new Tsparse_diagU2N
392 :    
393 :     * R/Ops.R ("-" (<sparseMatrix>)): use diagU2N()
394 :    
395 :     * src/chm_common.c (AS_CHM_FINISH): add note about problem
396 :     for triangular (diag = "U").
397 :    
398 : maechler 2115 2008-02-21 Martin Maechler <maechler@stat.math.ethz.ch>
399 :    
400 :     * R/Auxiliaries.R (as_Csparse2): drop this, replacing by
401 :     * R/bind.R: .Call(dense_to_Csparse, *)
402 :    
403 :     2008-02-20 Martin Maechler <maechler@stat.math.ethz.ch>
404 :    
405 :     * R/Matrix.R (Matrix): no longer use coercions to specific classes
406 :     (since we are discouraging them in user code).
407 :    
408 :     * tests/*.R: also replaces coercions to specific classes by
409 :     coercions to super classes.
410 :    
411 :     * R/denseMatrix.R (.dense2C): simplified by using forceSymmetric()
412 :    
413 :    
414 :     2008-02-19 Martin Maechler <maechler@stat.math.ethz.ch>
415 :    
416 :     * man/CAex.Rd: example: coerce to symmetric*, not dsC*
417 :    
418 :     * src/dense.c (dense_band): generalized from ddense_band
419 :    
420 :     * R/ddenseMatrix.R (.trilDense,.triuDense, .bandDense):
421 :     now for "denseMatrix" (instead of just "ddense*"); much
422 :     simplified setMethod()s for these.
423 :    
424 :     * src/dense.c (dense_to_symmetric): generalized from ddense_*
425 :    
426 :     2008-02-18 Martin Maechler <maechler@stat.math.ethz.ch>
427 :    
428 :     * R/AllGeneric.R: forceSymmetric() generic: fast no-checking
429 :     version of as(*, "symmetricMatric").
430 :    
431 :     * src/dense.c (ddense_to_symmetric): add 'symm_test' argument, and
432 :     * R/symmetricMatrix.R: set it TRUE in coercion to "symmetricMatrix"
433 :    
434 : maechler 2113 2008-02-16 Martin Maechler <maechler@stat.math.ethz.ch>
435 :    
436 :     * R/Matrix.R (subset.ij): utility, as first step to faster
437 :     M [ <ij-matrix> ] indexing.
438 :    
439 :     * R/Matrix.R (.M.sub.i.logical): M[ <logical> ] : try better.
440 :    
441 :     * src/dense.c (ddense_symmpart, ddense_skewpart): new functions
442 :     for more efficient symmpart() and skewpart() methods.
443 :    
444 :     * src/Mutils.c (equal_string_vectors): utility
445 :    
446 :     * src/dense.c (ddense_to_symmetric): new function used in
447 :    
448 :     * R/symmetricMatrix.R: setAs(., "symmetricMatrix")
449 :    
450 :     * R/sparseMatrix.R, et_al (isSymmetric): add '...' to formals, in
451 :     order to match the generic (and evade .local(..)).
452 :    
453 :     * R/dsCMatrix.R: dgC -> dsC: use C code!
454 :    
455 :     * NAMESPACE, R/AllGeneric.R (symmpart, skewpart): new functions
456 :     as per TODO
457 :    
458 :     * R/Auxiliaries.R (setZero, all0Matrix): new utilities
459 :    
460 :     * R/symmetricMatrix.R: obvious symmpart(), skewpart() methods
461 :    
462 :    
463 :     2008-02-15 Martin Maechler <maechler@stat.math.ethz.ch>
464 :    
465 :     * R/Ops.R (.Arith.Csparse): use diagU2N when needed in triangular
466 :    
467 :     * R/Auxiliaries.R (non0.i): take out of non0ind
468 :    
469 :     * R/ddenseMatrix.R (.trilDense, .triuDense, .bandDense):
470 :     make tril(), triu(), band() work for "matrix" and all "dense*"
471 :    
472 :     * R/triangularMatrix.R (.tri[lu].tr): need .diagU2N(*)
473 :     * tests/simple.R: test the fix above
474 :    
475 :     * R/sparseMatrix.R ([): simplification: no coerce to <general>
476 :     before we use as(., <Tsparse>)[...] anyway
477 :    
478 :     * R/Rsparse.R (.viaC.to.R): mostly instead of .viaC.to.dgR()
479 :    
480 :     * R/triangularMatrix.R (isTriangular): methods for all subclasses
481 :     instead of "triangularMatrix" -- just to disambiguate
482 :    
483 :     2008-02-14 Martin Maechler <maechler@stat.math.ethz.ch>
484 :    
485 :     * tests/Class+Meth.R (dotestMat): add m[FALSE, FALSE] { <-> TODO}
486 :     * tests/indexing.R: example that fails above
487 :    
488 : maechler 2110 2008-01-26 Martin Maechler <maechler@stat.math.ethz.ch>
489 :    
490 :     * R/Matrix.R (.M.sub.i.2col): fix for logical matrix indexing
491 :     * R/Tsparse.R (.TM.sub.i.2col, .TM.repl.i.2col): ditto;
492 :     now, M[lower.tri(M)] and M[lower.tri(M)] <- v work better
493 :    
494 :     * src/Tsparse.c (Tsparse_to_tCsparse): new fast utility.
495 :     * src/Tsparse.h, init.c: ditto
496 :     * R/Auxiliaries.R (isTriT): new; faster than going via Csparse
497 :     both isTriC() and isTriT() now return TRUE with "kind" or FALSE.
498 :     * R/sparseMatrix.R (isTriangular): hence simplified
499 :    
500 : maechler 2108 2008-01-24 Martin Maechler <maechler@stat.math.ethz.ch>
501 :    
502 :     * R/Ops.R (.Arith.Csparse): new utility factored out of former
503 :     <dgC> o <dgC>, extended for triangular and also used in <dtC> o <dtC>.
504 :    
505 : maechler 2106 2008-01-23 Martin Maechler <maechler@stat.math.ethz.ch>
506 :    
507 :     * tests/factorizing.R (checkSchur): and more tests for checking Schur()
508 :    
509 : maechler 2108 * inst/test-tools.R (isOrthogonal): new function; also file restructured
510 : maechler 2106
511 :     2008-01-22 Martin Maechler <maechler@stat.math.ethz.ch>
512 :    
513 :     * R/ngTMatrix.R: allow as(<numeric matrix>, "ngTMatrix") and hence
514 :     coercion to "nMatrix" and "pMatrix"
515 :    
516 :     * R/AllClass.R: "Schur" class; "number" class union
517 :     * man/number-class.Rd:
518 :     * man/Schur-class.Rd:
519 :    
520 :     * R/eigen.R (.dgeSchur): utility, and return "Schur" class
521 :     (.simpleSchur): Schur() method for diagonal matrices
522 :     (.triSchur): Schur() method for triangular matrices
523 :     (Schur.sym): Schur() for symmetric matrices {building on eigen()}.
524 :    
525 :    
526 :     2008-01-21 Martin Maechler <maechler@stat.math.ethz.ch>
527 :    
528 :     * src/dgCMatrix.c (dgCMatrix_QR): set @Dim slot (as per doc)
529 :    
530 : maechler 2105 2008-01-15 Martin Maechler <maechler@stat.math.ethz.ch>
531 :    
532 :     * R/CHMfactor.R (solve): method for b="numeric", but also b="ANY"
533 :     in order to ensure 'system = *' is not lost;
534 :     formals()$system instead of cut&paste.
535 :     * tests/factorizing.R: test solve(<CHM..>, <numeric>)
536 :    
537 : maechler 2102 2008-01-11 Martin Maechler <maechler@stat.math.ethz.ch>
538 : maechler 2096
539 : maechler 2105 * DESCRIPTION (Date): make ready for release --> 0.999375-4
540 : maechler 2096
541 : maechler 2102 * R/dgeMatrix.R: fix rcond() method for "dgeMatrix".
542 : maechler 2096
543 : maechler 2098 2007-12-08 Martin Maechler <maechler@stat.math.ethz.ch>
544 : maechler 2096
545 : maechler 2098 * R/pMatrix.R: as(*, "matrix") now returns 0/1 *integer* matrix,
546 :     and hence does as.vector(.).
547 :     * man/pMatrix-class.Rd: docs
548 :     * R/sparseMatrix.R: fix for printing "integer sparse"
549 :    
550 :     * tests/Class+Meth.R (tstMatrixClass): test M[FALSE], M[2] etc
551 :    
552 :     * R/Matrix.R and others: use "exact" function argument list for
553 :     both "[" : (x, i,j, ..., drop)
554 :     and "[<-" : (x, i,j, ..., value)
555 :    
556 :     * R/denseMatrix.R: M[i] and M[i] <- v (i vector) now work
557 :     * R/Tsparse.R (replTmat): ditto
558 :     * R/diagMatrix.R (replDiag): ditto
559 :     * R/Csparse.R (replCmat): ditto {was it worth the pain?}
560 :     * tests/indexing.R: testing the above
561 :    
562 : maechler 2096 2007-12-07 Martin Maechler <maechler@stat.math.ethz.ch>
563 :    
564 :     * R/sparseMatrix.R (cov2cor): method for sparse matrices
565 :    
566 :     * R/diagMatrix.R ([<-): fix D[ cbind(i,j) ] <- v
567 :    
568 :     * R/bind2.R: fix for Rsparse* and rbind2(dense,dense)
569 :    
570 :     * tests/Class+Meth.R: test cbind2, rbind2 and diag<-
571 :    
572 :     2007-12-06 Martin Maechler <maechler@stat.math.ethz.ch>
573 :    
574 :     * R/Matrix.R: "generic" cov2cor() method
575 :    
576 :     * R/nearPD.R: new 'only.values', 'keepDiag' arguments;
577 :     speed up Q %*% D %*% t(Q)
578 :     * tests/dpoMatrix.R: test nearPD()
579 :    
580 :     2007-12-05 Doug Bates and Martin Maechler
581 :    
582 :     * R/sparseMatrix.R: xtabs(*, sparse=.) function; an extention of
583 :     stats::xtabs() allowing to create sparse matrices.
584 :    
585 :     2007-10-08 Martin Maechler <maechler@stat.math.ethz.ch>
586 :    
587 :     * DESCRIPTION (Version): *-4 (released *-3 two days ago)
588 :    
589 : maechler 2081 2007-10-06 Martin Maechler <maechler@stat.math.ethz.ch>
590 :    
591 :     * R/pMatrix.R: solve(<Matrix>, <pMatrix>)
592 :    
593 :     2007-10-05 Martin Maechler <maechler@stat.math.ethz.ch>
594 :    
595 :     * R/LU.R: solve() method for "denseLU"
596 :    
597 :     2007-10-01 Martin Maechler <maechler@stat.math.ethz.ch>
598 :    
599 :     * DESCRIPTION (Version): 0.999375-3 preparing for release
600 :    
601 :     * R/AllGeneric.R: simplify if(.) .. else .. for R <= 2.5.1
602 :    
603 :     * R/Matrix.R (Matrix): .Internal(matrix(..)) different for R >= 2.7.0
604 :    
605 : maechler 2073 2007-09-26 Martin Maechler <maechler@stat.math.ethz.ch>
606 :    
607 :     * R/pMatrix.R (.m.mult.pMat): fix <matrix> %*% <pMatrix>,
608 :     thanks to Kasper Kristensen.
609 :     * tests/matprod.R: regression test for that.
610 :    
611 : bates 2069 2007-09-23 17:32 Douglas Bates <bates@stat.wisc.edu>
612 :    
613 :     * [r4778] R/AllGeneric.R: Check R version before defining generics for
614 :     primitives
615 :    
616 : maechler 2073 2007-09-13 Martin Maechler <maechler@stat.math.ethz.ch>
617 :    
618 :     * R/denseMatrix.R (rcond): method
619 :     * R/sparseQR.R (rcond): method, use x or t(x)
620 :    
621 :     2007-09-12 Martin Maechler <maechler@stat.math.ethz.ch>
622 :    
623 :     * R/dgeMatrix.R (rcond): method: work via qr.R() for non-square
624 :     matrices.
625 :     * R/sparseMatrix.R: Ditto for all other rcond() method definitions.
626 :    
627 :     * man/rcond.Rd: mention the more general definition, and add
628 :     example for non-square matrices.
629 :    
630 :     * man/chol.Rd: new file, for the S4 chol() generic and all methods.
631 :    
632 :     2007-09-11 Martin Maechler <maechler@stat.math.ethz.ch>
633 :    
634 :     * R/sparseQR.R: add qr.R() method [to be used for rcond()]
635 :    
636 : maechler 2062 2007-09-01 Martin Maechler <maechler@stat.math.ethz.ch>
637 :    
638 :     * R/Matrix.R ([<-): add (Matrix,missing,ANY,Matrix) etc
639 :     * tests/indexing.R: add new regression for the above cases.
640 :    
641 : maechler 2061 2007-08-30 Martin Maechler <maechler@stat.math.ethz.ch>
642 :    
643 :     * src/Mutils.h (__sun): clause for alloca.h on Solaris
644 :    
645 : maechler 2056 2007-08-16 Martin Maechler <maechler@stat.math.ethz.ch>
646 :    
647 :     * DESCRIPTION (Date, Version): 0.999375-2
648 :    
649 :     2007-08-15 Martin Maechler <maechler@stat.math.ethz.ch>
650 :    
651 :     * R/HBMM.R (readMM): make work for pattern matrices as well
652 :    
653 : bates 2050 2007-08-14 13:07 Douglas Bates <bates@stat.wisc.edu>
654 :    
655 :     * [r4730] src/Mutils.h: declare alloca
656 :     * [r4734] NAMESPACE, R/AllGeneric.R, R/Csparse.R, R/HBMM.R, R/Tsparse.R,
657 :     R/dgCMatrix.R, R/dgTMatrix.R, R/dsCMatrix.R, R/dsTMatrix.R,
658 :     man/externalFormats.Rd, src/Csparse.c, src/Csparse.h, src/DEPS.mkf,
659 :     src/HBMM.c, src/HBMM.h, src/Mutils.h, src/SOURCES_C.mkf, src/init.c,
660 :     src/mmio.c, src/mmio.h: Remove deprecated function writeHB and its
661 :     methods; switch writeMM to use CHOLMOD code; repair readMM
662 :    
663 : maechler 2048 2007-08-14 Martin Maechler <maechler@stat.math.ethz.ch>
664 :    
665 :     * R/nearPD.R, man/nearPD.Rd (nearPD): new function built on Jens
666 :     Oehlschlaegel's ... result type still to be discussed!
667 :    
668 : maechler 2043 2007-08-10 Martin Maechler <maechler@stat.math.ethz.ch>
669 :    
670 :     * man/image-methods.Rd: new, combining all image() methods
671 :    
672 :     2007-08-09 Martin Maechler <maechler@stat.math.ethz.ch>
673 :    
674 :     * R/dgCMatrix.R: define qr() and lu() methods for "sparseMatrix"
675 :     to work via dgC...
676 :    
677 :     * R/Matrix.R (Matrix): special treatment for "table" (S3)
678 :    
679 :     2007-08-07 Martin Maechler <maechler@stat.math.ethz.ch>
680 :    
681 :     * R/dgTMatrix.R (image): change defaults to
682 :     aspect = "iso", colorkey = FALSE
683 :    
684 : maechler 2039 2007-08-06 Martin Maechler <maechler@stat.math.ethz.ch>
685 :    
686 :     * src/dsyMatrix.c (dsyMatrix_matrix_mm): 'b' might be matrix;
687 :     must copy its *expanded* x slot before LAPACK call.
688 :    
689 :     * tests/matprod.R: test the last days' changes.
690 :    
691 : bates 2041 2007-08-06 16:43 Douglas Bates <bates@stat.wisc.edu>
692 :    
693 :     * [r4712] inst/include/Matrix_stubs.c: Change R_cholmod_printf in stubs
694 :     as well as in sources
695 : bates 2050 * [r4713] src/dsyMatrix.c: Duplicate the contents of the RHS before
696 :     Lapack call
697 : maechler 2043
698 : maechler 2036 2007-08-03 Martin Maechler <maechler@stat.math.ethz.ch>
699 :    
700 :     * R/Matrix.R (%*%, crossprod, tcrossprod): add method for
701 : maechler 2039 ("Matrix", "matrix") which is needed in some cases.
702 :     Ditto for solve().
703 : maechler 2036
704 :     * R/colSums.R (.as.dge.Fun): need ddenseMatrix methods to avoid
705 :     infinite recursion in dispatch for some cases.
706 :    
707 : bates 2041 2007-08-02 08:48 Martin Maechler <maechler@stat.math.ethz.ch>
708 : maechler 2036
709 : bates 2041 * [r4693] src/chm_common.c: R_cholmod_printf() instead of Rprintf() just
710 :     so pointers match
711 :    
712 : maechler 2024 2007-08-02 Martin Maechler <maechler@stat.math.ethz.ch>
713 :    
714 : maechler 2036 * DESCRIPTION (Date): set ready for release -- 0.999375-1
715 : maechler 2024
716 : bates 2020 2007-08-01 15:44 Douglas Bates <bates@stat.wisc.edu>
717 :    
718 :     * [r4686] inst/include/Matrix.h, inst/include/Matrix_stubs.c,
719 :     src/chm_common.c, src/chm_common.h: Change API for
720 :     numeric_as_chm_dense and N_AS_CHM_DN
721 : maechler 2024
722 : maechler 2018 2007-08-01 Martin Maechler <maechler@stat.math.ethz.ch>
723 :    
724 :     * src/dtrMatrix.c (dtrMatrix_matrix_mm): fix dimensionality check (!)
725 :     * tests/matprod.R: regr.test for it
726 :    
727 : maechler 2011 2007-07-20 Martin Maechler <maechler@stat.math.ethz.ch>
728 :    
729 :     * R/dMatrix.R: fix from Brian for Math2(., digits = "missing")
730 :     * tests/group-methods.R: and regression-test it
731 :    
732 : bates 2008 2007-07-19 19:45 Douglas Bates <bates@stat.wisc.edu>
733 :    
734 :     * [r4642] inst/include/Matrix.h, inst/include/Matrix_stubs.c,
735 :     inst/include/cholmod.h, src/chm_common.c, src/init.c: Export
736 :     triplet_to_sparse, documentation, use typedefs
737 : maechler 2011
738 : maechler 2005 2007-07-18 Martin Maechler <maechler@stat.math.ethz.ch>
739 :    
740 :     * man/dpoMatrix-class.Rd: added 'corMatrix' example
741 :    
742 :     * src/dsyMatrix.[ch] (dsyMatrix_as_matrix): new 'keep_dimnames' arg
743 :     * src/dtrMatrix.[ch] (dtrMatrix_as_matrix): ditto
744 :     * src/init.c, R/dsyMatrix.R, R/dtrMatrix.R, R/lgTMatrix.R: ditto
745 :    
746 :     * R/lsparseMatrix.R: bug fix in "all" method
747 :     * R/Ops.R (.do.Logic.lsparse): "|" bug in borderline case
748 :    
749 :     * R/dsyMatrix.R (coerce->dsTMatrix): (i,j) slots should *not* have names
750 :     * R/ngTMatrix.R (coerce->ngTMatrix): ditto;
751 :     + matrix |-> nMatrix coercion
752 :     * R/pMatrix.R: + setAs() to dMatrix and from nMatrix
753 :     * man/pMatrix-class.Rd: ditto
754 :    
755 :     * R/Matrix.R (Summary): method for non-dMatrix
756 :    
757 :     * tests/Class+Meth.R (extraValid): new check about "dirty" slots
758 :     * tests/Class+Meth.R (tstMatrixClass): test norm(.);
759 :     test all Summary methods.
760 :    
761 :     2007-07-16 Martin Maechler <maechler@stat.math.ethz.ch>
762 :    
763 :     * R/dgeMatrix.R (norm, rcond): methods for 'matrix'
764 :    
765 :     2007-07-14 Martin Maechler <maechler@stat.math.ethz.ch>
766 :    
767 :     * R/sparseMatrix.R (norm): simple methods for sparseMatrix
768 :    
769 :     * R/pMatrix.R (t?crossprod): methods for pMatrix
770 :    
771 : bates 1987 2007-07-10 Douglas Bates <bates@stat.wisc.edu>
772 :    
773 :     * src/dgeMatrix.c (dgeMatrix_colsums): Get the logic straight.
774 :    
775 : bates 1975 2007-07-09 20:45 Douglas Bates <bates@stat.wisc.edu>
776 :    
777 :     * [r4579] src/dgeMatrix.c: Untangle horrible code in dgeMatrix_colsums
778 : maechler 2005 trying to fix a subtle bug - which has been somewhere else.
779 : bates 1975
780 :     2007-07-09 19:43 Martin Maechler <maechler@stat.math.ethz.ch>
781 :    
782 :     * [r4578] src/dgeMatrix.c: "cleaned" dgeMatrix_colsums() - but did not
783 :     solve the bug
784 :    
785 : maechler 1968 2007-07-08 Martin Maechler <maechler@stat.math.ethz.ch>
786 : bates 1964
787 : maechler 1968 * src/dgCMatrix.c (compressed_to_TMatrix):
788 :    
789 :     2007-07-07 Martin Maechler <maechler@stat.math.ethz.ch>
790 :    
791 :     * src/Csparse.c (Rsparse_validate): new, to have some validity
792 :     checking for RsparseMatrix
793 :     * src/dgCMatrix.c (xRMatrix_validate): ditto
794 :     * src/dtCMatrix.c (tRMatrix_validate): ditto
795 :    
796 :     2007-07-07 Douglas Bates <bates@stat.wisc.edu>
797 :    
798 : bates 1964 * [r4567] R/AllClass.R: Slots already in RsparseMatrix were redefined in
799 :     lgRMatrix
800 :     * [r4568] DESCRIPTION: Prepare for bug-fix release
801 : bates 1966 * [r4570] src/CHOLMOD/Check/cholmod_write.c: Include cholmod_matrixops.h
802 :     for declaration of cholmod_symmetry
803 : maechler 1968
804 : maechler 1961 2007-07-06 Martin Maechler <maechler@stat.math.ethz.ch>
805 :    
806 :     * DESCRIPTION (Version): 0.999375 merged into the trunk; ready for
807 :     release.
808 :    
809 : maechler 1960 2007-07-06 14:11 Douglas Bates <bates@stat.wisc.edu>
810 :    
811 :     * [r4559] src/iohb.c, src/iohb.h: Remove Harwell-Boeing input/output
812 :     functions - no longer used
813 :     * [r4560] src/HBMM.c, src/Mutils.c, src/dgTMatrix.c, src/dgeMatrix.c,
814 :     src/dspMatrix.c, src/dsyMatrix.c, src/dtCMatrix.c,
815 :     src/factorizations.c, src/sparseQR.c: Replace most calls to Calloc by
816 :     Alloca
817 :    
818 :     2007-07-06 13:14 Martin Maechler <maechler@stat.math.ethz.ch>
819 :    
820 :     * [r4558] inst/doc/Comparisons.Rnw, src/CHMfactor.c, src/Csparse.c,
821 :     src/Tsparse.c, src/chm_common.c, src/chm_common.h, src/dense.c,
822 :     src/dgCMatrix.c, src/dsCMatrix.c, src/dtTMatrix.c, src/sparseQR.c,
823 :     src/t_gCMatrix_colSums.c: more R_CheckStack()s
824 :    
825 :     2007-07-05 18:12 Douglas Bates <bates@stat.wisc.edu>
826 :    
827 :     * [r4550] inst/include/Matrix.h: Add the macro N_AS_CHM_DN to "alloca"
828 :     the required amount of memory then call M_numeric_as_chm_dense.
829 :     * [r4556] src/Mutils.h, src/dgCMatrix.c: Define and use the Alloca macro
830 :     (like Calloc but calling alloca)
831 :    
832 : maechler 1947 2007-07-05 Martin Maechler <maechler@stat.math.ethz.ch>
833 :    
834 :     * R/sparseMatrix.R (printSpMatrix): renamed from prSpMatrix()
835 :     and extended with more sophisticated 'col.names' option.
836 :     * NAMESPACE: export printSparseMatrix()
837 :     * man/printSpMatrix.Rd: document, incl. examples
838 :    
839 : maechler 1960 2007-07-04 16:21 Douglas Bates <bates@stat.wisc.edu>
840 :    
841 :     * [r4543] src/cs_utils.c, src/cs_utils.h, src/dgCMatrix.c,
842 :     src/dtCMatrix.c, src/sparseQR.c: CSP typedef for *cs and macro
843 :     AS_CSP. API change - pass the empty structure to Matrix_as_cs.
844 :    
845 : maechler 1945 2007-07-04 Martin Maechler <maechler@stat.math.ethz.ch>
846 :    
847 :     * DESCRIPTION (Version): 0.99875-4
848 :    
849 :     * tests/Class+Meth.R (tstMatrixClass): add dimnames, and hence test
850 :     some dimnames perservation.
851 :    
852 :     * R/dsTMatrix.R (t-method): keep dimnames
853 :     * R/dtTMatrix.R: ditto
854 :    
855 :     * R/sparseMatrix.R (prSpMatrix): print colnames when non-trivial
856 :     and ncol(.) < 10
857 :    
858 :     * src/cs_utils.c: drop check_class() and use Matrix_check_class()
859 :     from Mutils.h
860 :    
861 :     * src/lgCMatrix.c ([ln]csc_to_matrix): no longer lose dimnames,
862 :     e.g. in as(<ngCMatrix>, "matrix")
863 :    
864 : maechler 1960 2007-07-01 13:27 Douglas Bates <bates@stat.wisc.edu>
865 :    
866 :     * [r4529] .: Create a branch for the API changes from the 0.99875
867 :     series to the 0.999375 series
868 :     * [r4530] DESCRIPTION, inst/include/Matrix.h,
869 :     inst/include/Matrix_stubs.c, src/CHMfactor.c, src/Csparse.c,
870 :     src/Mutils.h, src/Tsparse.c, src/chm_common.c, src/chm_common.h,
871 :     src/dense.c, src/dgCMatrix.c, src/dsCMatrix.c, src/dtTMatrix.c,
872 :     src/t_gCMatrix_colSums.c: API change - pass the empty structure to the
873 :     as_cholmod_x functions
874 :    
875 :     2007-06-30 09:05 Martin Maechler <maechler@stat.math.ethz.ch>
876 :    
877 :     * [r4527] trunk/Matrix/DESCRIPTION, trunk/Matrix/NAMESPACE,
878 :     trunk/Matrix/inst/doc/Comparisons.Rnw: add session- and hardware-info
879 :     to Comparisons
880 :    
881 :     >>>>>>> .merge-right.r4561
882 : maechler 1932 2007-06-29 Martin Maechler <maechler@stat.math.ethz.ch>
883 :    
884 :     * DESCRIPTION (Version): 0.99875-3 ready to be released.
885 :    
886 :     * R/sparseMatrix.R (spMatrix): make spMatrix(3,4) working
887 :    
888 :     * R/AllGeneric.R: set "Math" (and "Math2") group generics in a way
889 :     that should also work in a future version of R.
890 :    
891 : maechler 1922 2007-06-21 Martin Maechler <maechler@stat.math.ethz.ch>
892 :    
893 :     * NAMESPACE, R/AllClass.R: "xsparseVector" class union.
894 :    
895 :     * R/sparseVector.R: more *sparseVector coercions, notably for
896 :     non - double ones.
897 :    
898 : maechler 1911 2007-06-19 Martin Maechler <maechler@stat.math.ethz.ch>
899 :    
900 :     * R/colSums.R: new file for all (col|row)(Sums|Means) methods,
901 :     notably the new ones building on the new .Call(.)s:
902 :    
903 :     * src/dgCMatrix.c (DEF_gCMatrix_COLSUMS): use to define
904 :     all 4 of [dlin]gCMatrix_colSums().
905 :    
906 : bates 1909 2007-06-18 16:12 Douglas Bates <bates@stat.wisc.edu>
907 :    
908 :     * [r4472] src/Syms.h, src/init.c: Added Matrix_lengthSym
909 :     * [r4473] src/dgCMatrix.c: Modified dgCMatrix_colSums for sparseVector
910 :     result
911 : maechler 1911
912 : maechler 1903 2007-06-16 Martin Maechler <maechler@stat.math.ethz.ch>
913 :    
914 : maechler 1904 * R/kronecker.R: fix typo (could lead to inf.recursion)
915 :     * test/simple.R: testing that
916 :    
917 : maechler 1903 * R/sparseMatrix.R (prSpMatrix): change to be used as print()
918 : maechler 1922 method as well (which can have arguments, show() can't).
919 : maechler 1903
920 : bates 1902 2007-06-16 15:52 Douglas Bates <bates@stat.wisc.edu>
921 :    
922 :     * [r4466] R/dgCMatrix.R, src/dgCMatrix.c, src/dgCMatrix.h, src/init.c:
923 :     added dgCMatrix_colSums for [col,row][Sums,Means]
924 :    
925 : bates 1899 2007-06-15 23:15 Douglas Bates <bates@stat.wisc.edu>
926 : bates 1897
927 :     * [r4460] R/sparseMatrix.R, man/dgCMatrix-class.Rd, src/dgCMatrix.c,
928 :     src/dgCMatrix.h, src/init.c: added lm.fit.sparse (unexported),
929 :     coercion of "factor" to "dgCMatrix" and dgCMatrix_cholsol
930 :     * [r4461] R/AllClass.R, man/sparseMatrix-class.Rd: draft "indicators"
931 :     class
932 : bates 1899 * [r4463] R/sparseMatrix.R, man/dgCMatrix-class.Rd,
933 :     man/sparseMatrix-class.Rd: Don't need an "indicators" class - use the
934 :     row names to store the levels - duh! Added an example.
935 : maechler 1903
936 : maechler 1893 2007-06-14 Martin Maechler <maechler@stat.math.ethz.ch>
937 :    
938 :     * src/Csparse.c (Csparse_validate): check for *repeated* entries
939 :     thanks to example from Christian Buchta; with a test here:
940 :     * tests/simple.R:
941 :    
942 : maechler 1886 2007-06-07 Martin Maechler <maechler@stat.math.ethz.ch>
943 :    
944 :     * R/Auxiliaries.R (callGeneric): another fix, needed for some cases
945 :     of colSums(*, sparseResult = TRUE)
946 :    
947 : maechler 1883 2007-06-06 Martin Maechler <maechler@stat.math.ethz.ch>
948 :    
949 :     * R/lsparseMatrix.R, R/ldenseMatrix.R (all, any): change default to
950 :     'na.rm = FALSE' as "everywhere" else in R.
951 :    
952 : bates 1877 2007-06-05 Douglas Bates <bates@stat.wisc.edu>
953 :    
954 : bates 1878 * [r4421] src/CSparse_install.sh: Modify for new organization of
955 : maechler 1883 CSparse package
956 : bates 1877 * [r4425] src/UFsparse_download.sh: Update to version 3.0.0 of
957 :     SuiteSparse
958 :     * [r4426] src/Makefile: add ./UFconfig to the include path for
959 :     compilation
960 : maechler 1883 * [r4427] src/cs.[ch]: update to CSparse version 2.2.0
961 :     * [r4428] inst/doc/UFsparse/* src/{AMD,CHOLMOD,COLAMD}/*
962 :     src/UFconfig/UFconfig.h: Update to version 3.0.0 of SuiteSparse
963 :    
964 : maechler 1870 2007-06-05 Martin Maechler <maechler@stat.math.ethz.ch>
965 :    
966 :     * R/Auxiliaries.R (emptyColnames): + argument msg.if.not.empty, used in
967 :     * R/sparseMatrix.R (prSpMatrix): now gives a message about
968 :     suppressed column names.
969 :    
970 : bates 1868 2007-06-04 17:13 Douglas Bates <bates@stat.wisc.edu>
971 :    
972 :     * [r4418] src/Csparse.c, src/HBMM.c, src/Mutils.c, src/Mutils.h,
973 :     src/Tsparse.c, src/chm_common.c, src/chm_common.h, src/dgCMatrix.c,
974 :     src/dgeMatrix.c, src/dpoMatrix.c, src/dpoMatrix.h, src/dppMatrix.c,
975 :     src/dppMatrix.h, src/dsCMatrix.c, src/dspMatrix.c, src/dspMatrix.h,
976 :     src/dsyMatrix.c, src/dsyMatrix.h, src/dtpMatrix.c, src/dtrMatrix.c:
977 :     Remove warnings after change to const char* CHAR
978 :    
979 :     2007-06-04 17:11 Douglas Bates <bates@stat.wisc.edu>
980 :    
981 :     * [r4417] inst/include/Matrix_stubs.c, inst/include/cholmod.h: Corrected
982 :     type of M_cholmod_ssmult
983 :    
984 : bates 1863 2007-06-03 14:42 Douglas Bates <bates@stat.wisc.edu>
985 :    
986 :     * [r4412] inst/include/Matrix_stubs.c, inst/include/cholmod.h,
987 :     src/init.c: Yet another cholmod export - cholmod_ssmult
988 :    
989 : maechler 1855 2007-05-23 Martin Maechler <maechler@stat.math.ethz.ch>
990 :    
991 :     * NAMESPACE: exported drop0(), since
992 :     * man/drop0.Rd: I have seen several cases, I really wanted to use
993 :     it, so our users may want too.
994 :    
995 :     2007-05-22 Martin Maechler <maechler@stat.math.ethz.ch>
996 :    
997 :     * man/colSums.Rd: separately document colSums() etc, since these
998 :     have the extra argument 'sparseResult'.
999 :    
1000 : maechler 1852 2007-05-21 Martin Maechler <maechler@stat.math.ethz.ch>
1001 :    
1002 :     * R/sparseMatrix.R (spMatrix): utility (T)sparse Matrix constructor;
1003 :     * man/spMatrix.Rd: docu., including examples
1004 :    
1005 :     * R/Auxiliaries.R (sp.colMeans): etc, using a patched callGeneric(),
1006 :     in order to make colMeans() etc fast *and* correct.
1007 :     * R/sparseVector.R (replSPvec): "[<-" functionality for
1008 :     sparseVectors; tested in
1009 :     * tests/simple.R:
1010 :    
1011 :     2007-05-19 Martin Maechler <maechler@stat.math.ethz.ch>
1012 :    
1013 :     * R/sparseMatrix.R (print.sparseSummary): and summary() method for
1014 :     (very) sparse Matrices; output similar to Matlab's print().
1015 :    
1016 : bates 1847 2007-05-17 Douglas Bates <bates@stat.wisc.edu>
1017 :    
1018 :     * src/HBMM.c (Matrix_writeMatrixMarket): Write 1-based, not
1019 :     0-based, indices (Jose Quesada <quesada@gmail.com>).
1020 :    
1021 : bates 1844 2007-05-16 Douglas Bates <bates@stat.wisc.edu>
1022 :    
1023 :     * R/CHMfactor.R: Added solve methods for a CHMfactor object.
1024 :    
1025 : maechler 1845 2007-05-16 Martin Maechler <maechler@stat.math.ethz.ch>
1026 :    
1027 :     * R/Auxiliaries.R (sparsapply): new utility, much faster than
1028 :     tapply1() for large sparse matrices.
1029 :    
1030 :     2007-05-15 Martin Maechler <maechler@stat.math.ethz.ch>
1031 :    
1032 :     * R/Matrix.R (dim<-): reshape now via sparseVector.
1033 :    
1034 :     * R/sparseVector.R: methods and function for
1035 :     * R/AllClass.R: new "sparseVector" class and daughters.
1036 :     * NAMESPACE: export new classes
1037 :    
1038 : maechler 1837 2007-05-14 Martin Maechler <maechler@stat.math.ethz.ch>
1039 :    
1040 :     * DESCRIPTION (Version): 0.99875-1
1041 :     * src/Makefile.win: also remove Lapack code from here (cf. 04-25).
1042 :    
1043 : maechler 1834 2007-05-11 Martin Maechler <maechler@stat.math.ethz.ch>
1044 :    
1045 :     * R/Tsparse.R ([, Tsparse): fix last case: *duplicated*, symmetric
1046 :     indexing
1047 :     * tests/indexing.R: test set for that.
1048 :    
1049 : maechler 1833 2007-05-08 Martin Maechler <maechler@stat.math.ethz.ch>
1050 :    
1051 :     * R/Tsparse.R (replTmat): fix the case of *duplicated* index
1052 :     entries.
1053 :     * tests/indexing.R(out): add regression test for it
1054 :    
1055 :     2007-04-30 Martin Maechler <maechler@stat.math.ethz.ch>
1056 :    
1057 :     * R/(l(dense|sparse))?Matrix.R (!): use 'x', not 'e1' as argument
1058 :     name for "!" method definitions.
1059 :    
1060 : maechler 1829 2007-04-26 Martin Maechler <maechler@stat.math.ethz.ch>
1061 :    
1062 :     * R/Tsparse.R (intI): new utility, used for "[" :
1063 :     Cleanup up there, and fixes for duplicated indices - more TODO!
1064 :    
1065 :     * tests/indexing.R(out): more tests
1066 :    
1067 : bates 1827 2007-04-25 Douglas Bates <bates@stat.wisc.edu>
1068 :    
1069 :     * DESCRIPTION,src/Makefile: require R>= 2.5.0 and remove Lapack
1070 :     code that is now part of the R Lapack library.
1071 : maechler 1829
1072 : bates 1827 * src/init.c,inst/include/{Matrix_stubs.c,cholmod.h}:export
1073 :     cholmod_factorize_p (used in lme4 for GLMMs and NLMMs).
1074 :    
1075 : maechler 1829 2007-04-21 Martin Maechler <maechler@stat.math.ethz.ch>
1076 :    
1077 :     * R/Matrix.R (image): method for all Matrices, not just sparse ones.
1078 :    
1079 :     2007-04-17 Martin Maechler <maechler@stat.math.ethz.ch>
1080 :    
1081 :     * R/Auxiliaries.R (tapply1): unname(.) -> colSums() etc don't end
1082 :     up with extraneous names '0'...'<n-1>'
1083 :    
1084 : maechler 1825 2007-04-12 Martin Maechler <maechler@stat.math.ethz.ch>
1085 :    
1086 :     * R/dgTMatrix.R (mat2dgT): care about NAs
1087 :    
1088 :     2007-04-11 Martin Maechler <maechler@stat.math.ethz.ch>
1089 :    
1090 :     * R/kronecker.R: triangularity preserving methods
1091 :    
1092 : maechler 1803 2007-03-27 Martin Maechler <maechler@stat.math.ethz.ch>
1093 :    
1094 :     * R/kronecker.R: new file collecting kronecker() methods in one
1095 :     place. Goal: become much faster!
1096 :    
1097 : maechler 1799 2007-03-23 Martin Maechler <maechler@stat.math.ethz.ch>
1098 :    
1099 :     * src/dtCMatrix.c (dtCMatrix_solve): use the new code from Kasper
1100 :     Kristensen based cs_spsolve() instead of _lsolve & _usolve which
1101 :     can be much faster.
1102 :    
1103 :     * tests/matprod.R: add regression tests for these (upper & lower).
1104 :    
1105 :     2007-03-19 Martin Maechler <maechler@stat.math.ethz.ch>
1106 :    
1107 :     * R/Matrix.R (diff): method for our Matrices.
1108 :    
1109 :     * R/sparseMatrix.R (isDiagonal): check dim()!
1110 :    
1111 :     2007-03-17 Martin Maechler <maechler@stat.math.ethz.ch>
1112 :    
1113 :     * R/Matrix.R (dim<-): new method for "reshape()" built on a
1114 :     proposal from Tamas Papp.
1115 :    
1116 :     2007-03-16 Martin Maechler <maechler@stat.math.ethz.ch>
1117 :    
1118 :     * R/AllGeneric.R: remove all if(!isGeneric(.)) clauses
1119 :    
1120 :     * R/zzz.R (.onLoad, .onUnload): do *not* leave bind_activation(TRUE);
1121 : maechler 1803 rather define and export cBind() and rBind() only.
1122 :     --> useRs *must* change code that used to have cbind()/rbind() !!
1123 : maechler 1799
1124 : maechler 1803 * R/bind.R: change tests from cbind() to cBind() and similarly to rBind()
1125 :     * R/bind.Rout.save: ditto
1126 : maechler 1799
1127 : bates 1787 2007-02-16 Douglas Bates <bates@r-project.org>
1128 :    
1129 :     * DESCRIPTION (Date, Version): 0.9975-11 with new date
1130 :     * src/dgCMatrix.c (R_to_CMatrix, compressed_to_TMatrix): remove
1131 :     const modifier on declaration of the array 'valid'
1132 :    
1133 : bates 1786 2007-02-12 Douglas Bates <bates@stat.wisc.edu>
1134 :    
1135 :     * R/CHMfactor.R: Add image method (coercion to sparseMatrix).
1136 :    
1137 : maechler 1765 2007-02-05 Martin Maechler <maechler@stat.math.ethz.ch>
1138 :    
1139 : maechler 1768 * DESCRIPTION (Date, Version): 0.9975-10 with new date.
1140 :    
1141 : maechler 1767 * R/Ops.R (Arith): make sure Csparse o Csparse also works for e.g. ntCMatrix
1142 :     * tests/simple.R: test the above and some of these coercions:
1143 :    
1144 :     * R/nsparseMatrix.R: coercing "Csparse" to "lsparseMatrix";
1145 :     be careful to avoid infinite recursion, using new coercions in
1146 :     * R/ngCMatrix.R and nsC... and ntC...
1147 :     * R/lsparseMatrix.R: ditto
1148 :    
1149 : maechler 1765 * R/SparseM-conv.R: more conversion, notably for triplet matrices.
1150 :    
1151 : maechler 1767 * src/dgCMatrix.c (R_to_C_Matrix): port Doug's fix and
1152 :     * R/Rsparse.R: reactivate .Call()s
1153 : maechler 1765
1154 : maechler 1767 * tests/Class+Meth.R: a bit more on actual classes
1155 :    
1156 :     2007-02-04 Douglas Bates <bates@stat.wisc.edu>
1157 :    
1158 :     * src/dgCMatrix.c (compressed_to_TMatrix): fix memory bug using strdup()
1159 :    
1160 : maechler 1760 2007-02-03 Martin Maechler <maechler@stat.math.ethz.ch>
1161 : maechler 1758
1162 :     * DESCRIPTION (Version): 0.9975-10 to upload
1163 :    
1164 : maechler 1760 * tests/Class+Meth.R (tstMatrixClass): require coercions to
1165 :     specific classes less unconditionally.
1166 :    
1167 :     * R/Auxiliaries.R: get rid of as_Tsparse() and as_Rsparse()
1168 :    
1169 :     * R/Tsparse.R (triu): etc, use as(*, "TsparseMatrix") instead of as_Tsparse()
1170 :    
1171 :     * R/Rsparse.R (.R.2.T): R-level workaround using compressed_to_TMatrix.
1172 : maechler 1758 * R/Rsparse.R (.R.2.C): R-level workaround since C-level
1173 :     R_to_CMatrix segfaults on one platform.
1174 : maechler 1760 Eliminate most coercion method to *specific* classes, and replace
1175 :     with virtual classes coercions.
1176 : maechler 1758
1177 : maechler 1760
1178 : maechler 1758 2007-02-01 Martin Maechler <maechler@stat.math.ethz.ch>
1179 :    
1180 :     * src/init.c: export the CHM...._validate() placeholders, since
1181 :     they *are* called.
1182 :    
1183 : maechler 1760 * tests/Class+Meth.R (classCanCoerce): and starting to test
1184 : maechler 1758 all as(<from>, <to>)
1185 :    
1186 : maechler 1751 2007-01-30 Martin Maechler <maechler@stat.math.ethz.ch>
1187 :    
1188 :     * R/Tsparse.R ([): more care when subsetting triangular Tsparse
1189 :     * tests/indexing.R: tested now
1190 :     * tests/indexing.Rout.save: updated
1191 :    
1192 :     * src/Csparse.c (Csparse_to_dense): use Rkind = -1 for PATTERN to
1193 :     * src/chm_common.c (chm_dense_to_SEXP): return "ngeMatrix" when
1194 :     appropriate.
1195 :    
1196 :     * NAMESPACE: export a trivial
1197 :     * R/Matrix.R: drop() Matrix-method
1198 :    
1199 :     * R/AllClass.R: moved all prototypes to virtual super classes.
1200 :    
1201 :     * R/Rsparse.R: many more coercions to have less exceptions in
1202 :     * tests/Class+Meth.R:
1203 :    
1204 :     * R/Ops.R (Compare): tweak for case with NA
1205 :     * tests/simpl.R: hence another 'FIXME' eliminated
1206 :    
1207 : maechler 1747 2007-01-29 Martin Maechler <maechler@stat.math.ethz.ch>
1208 :    
1209 : maechler 1748 * R/diagMatrix.R (solve): the obvious methods for diagonalMatrix
1210 :     objects.
1211 :    
1212 : maechler 1747 * tests/Class+Meth.R (tstMatrixClass): now testing diag(), nnzero(),
1213 :     and more of "!", "&", "|", all, any; coercions
1214 :    
1215 :     * R/Rsparse.R: many coercions (which enable quite a few other
1216 :     methods), thanks to enhancements in
1217 :     * src/dgCMatrix.c (R_to_CMatrix): new, and
1218 :     * src/dgCMatrix.c (compressed_to_TMatrix): now for (d,l,n) ,
1219 :     symmetric & triangular and ..RMatrix objects.
1220 :    
1221 :     * src/TMatrix_as.c (Matrix_T_as_DENSE,Matrix_T_as_GENERAL):
1222 :     renamed file from src/dsTMatrix.c;
1223 :     now dealing with symmetric and triangular Tsparse coercions, both
1224 :     to dense and general.
1225 :    
1226 :     2007-01-27 Martin Maechler <maechler@stat.math.ethz.ch>
1227 :    
1228 :     * src/dsTMatrix.c: has now "l" and "n" methods besides the "d" ones.
1229 :    
1230 :     * R/Ops.R (Arith): <dgCMatrix> o <numeric> now remains sparse
1231 :     where sensible when the <numeric> is of length > 1.
1232 :    
1233 :     2007-01-26 Martin Maechler <maechler@stat.math.ethz.ch>
1234 :    
1235 :     * R/Matrix.R ([<-): for M[] <- value: fix length
1236 :    
1237 :     2007-01-25 Martin Maechler <maechler@stat.math.ethz.ch>
1238 :    
1239 :     * R/Auxiliaries.R (n2l_Matrix): new, to be used in
1240 :     * R/ndenseMatrix.R: new coercions n* -> l*
1241 :    
1242 : maechler 1738 2007-01-22 Martin Maechler <maechler@stat.math.ethz.ch>
1243 :    
1244 :     * R/triangularMatrix.R: new file; simple triu() and tril() methods.
1245 :    
1246 :     * R/Ops.R ("Logic"): and other "Ops", many updates
1247 :    
1248 :     2007-01-18 Martin Maechler <maechler@stat.math.ethz.ch>
1249 :    
1250 :     * src/Mutils.h (SET_DimNames): new utility
1251 :    
1252 :     * R/Auxiliaries.R (nnzero): improved and now exported via
1253 :    
1254 :     * NAMESPACE: + nnzero(); length() == prod(dim(.)) method for all "Matrix" objects
1255 :    
1256 : maechler 1725 2007-01-17 Martin Maechler <maechler@stat.math.ethz.ch>
1257 :    
1258 :     * R/diagMatrix.R (!): fix typo.
1259 :    
1260 :     2007-01-16 Martin Maechler <maechler@stat.math.ethz.ch>
1261 :    
1262 :     * R/Auxiliaries.R (as_Csparse): and quite a few others:
1263 :     allow to pass class definition --> speedup
1264 :     * R/sparseMatrix.R: apply the above
1265 :    
1266 :     * R/Csparse.R: coercion Csparse* to dense* now preserves shape properties.
1267 :    
1268 :     * src/Mutils.h (mMatrix_as_geMatrix): new, based on
1269 :     * src/Mutils.c (dup_mMatrix_as_geMatrix): new; generalization of
1270 :     old dup_mMatrix_as_dgeMatrix), eliminating a long-standing "FIXME".
1271 :    
1272 :     * src/dense.c (dense_to_Csparse): use new mMatrix_as_geMatrix()
1273 :    
1274 :     * R/denseMatrix.R (.dense2C): based on dense_to_Csparse: name it,
1275 :     and use it for "sparse*" as well, since it's faster than the
1276 :     as_Csparse(.) way.
1277 :    
1278 :     2007-01-15 Martin Maechler <maechler@stat.math.ethz.ch>
1279 :    
1280 :     * R/Ops.R ("Logic"): more methods, notably an <lgC> o <lgC> one.
1281 :    
1282 : maechler 1724 2007-01-12 Martin Maechler <maechler@stat.math.ethz.ch>
1283 :    
1284 :     * R/Tsparse.R (.TM.repl.i.2col): new internal function to be used
1285 :     as method for M[ ij ] <- v
1286 :     * R/Csparse.R:: go via Tsparse for "M[ij] <- v"
1287 :    
1288 :     * R/Ops.R: "Compare" for (C|R)sparse: need pointer slot for all
1289 :     FALSE answer
1290 :    
1291 :     * R/Csparse.R (replCmat): fix the "all non-zero" case with reordering
1292 :     * tests/indexing.R: test it, and some of the above
1293 :    
1294 :     2007-01-05 Martin Maechler <maechler@stat.math.ethz.ch>
1295 :    
1296 :     * R/Auxiliaries.R (is_duplicatedT): new utility
1297 :    
1298 : bates 1716 2007-01-05 Douglas Bates <bates@stat.wisc.edu>
1299 :    
1300 :     * src/init.c (R_init_Matrix): export cholmod_scale
1301 :    
1302 : maechler 1724 2006-12-30 Martin Maechler <maechler@stat.math.ethz.ch>
1303 :    
1304 :     * R/zzz.R (tmp): for R >= 2.5.0, extend formals of our
1305 :     base::as.matrix to (x, ...)
1306 :    
1307 : maechler 1714 2006-12-28 Martin Maechler <maechler@stat.math.ethz.ch>
1308 :    
1309 :     * R/Ops.R ("Arith" etc): move almost all "Ops" methods to new R
1310 :     file; start using "Logic", hence
1311 :    
1312 :     * DESCRIPTION (Depends): R >= 2.4.1 (since we want "Logic")
1313 :     * NAMESPACE: import and export "Logic"
1314 :    
1315 :     2006-12-27 Martin Maechler <maechler@stat.math.ethz.ch>
1316 :    
1317 :     * src/zpotfr.f and dependencies: use LAPACK 3.1 version
1318 :     only needed previously to R version 2.5.0.
1319 : maechler 1724
1320 : maechler 1710 2006-12-26 Martin Maechler <maechler@stat.math.ethz.ch>
1321 :    
1322 :     * DESCRIPTION (Date, Version): 0.9975-8, ready for release
1323 :    
1324 :     * R/Tsparse.R (replTmat): fix subassignment of triangular
1325 :     * R/Csparse.R (replCmat): ditto
1326 :     * tests/indexing.R: more tests, incl the above fix
1327 :    
1328 :     2006-12-23 Martin Maechler <maechler@stat.math.ethz.ch>
1329 :    
1330 :     * R/Auxiliaries.R (drop0): extend for non CSparse
1331 :     * R/Auxiliaries.R (diagU2N): should work for all sparseMatrix
1332 :    
1333 :     * src/Csparse.c (Csparse_to_Tsparse, Csparse_general_to_symmetric):
1334 :     use uplo correctly (!); other places: use uplo_P() macro
1335 :    
1336 :     * R/Csparse.R (replCmat): call diagU2N() when needed
1337 :     * R/Tsparse.R (replTmat): ditto
1338 :    
1339 :     * src/dtCMatrix.c (tCMatrix_validate): new
1340 :     * src/dtTMatrix.c (tTMatrix_validate): new, used in
1341 :     * R/AllClass.R: for validity of dtC, dsC, and dtT, dsT.
1342 :    
1343 :     * R/diagMatrix.R (replDiag): to use in [<-
1344 :    
1345 : maechler 1708 2006-12-22 Martin Maechler <maechler@stat.math.ethz.ch>
1346 :    
1347 :     * R/Auxiliaries.R (as_Csparse2, as_geSimpl): new functions;
1348 :     also more general diagU2N().
1349 :    
1350 :     2006-12-21 Martin Maechler <maechler@stat.math.ethz.ch>
1351 :    
1352 :     * R/bind2.R: new file for all cbind2(), rbind() methods moved here
1353 :     from R/<foo>Matrix.R files. Better diagonal & improved sparse methods.
1354 :    
1355 : maechler 1707 2006-12-20 Martin Maechler <maechler@stat.math.ethz.ch>
1356 :    
1357 :     * tests/bind.R: a few more cases
1358 :     * R/Auxiliaries.R (.M.kind): also work for atomic vectors
1359 :    
1360 :     * R/denseMatrix.R (cbind2/rbind2): moved here (and generalized) from
1361 :     * R/ddenseMatrix.R (cbind2/rbind2)
1362 :     * R/Tsparse.R (replTmat): final(?!) fix for "[<-" ..
1363 :     * tests/indexing.R
1364 :     * tests/indexing.Rout.save: updated
1365 :    
1366 :     2006-12-18 Martin Maechler <maechler@stat.math.ethz.ch>
1367 :    
1368 :     * R/Tsparse.R (replTmat): fixed a remaining "[<-" bug in
1369 :     * tests/indexing.R
1370 :    
1371 : maechler 1705 2006-12-15 Martin Maechler <maechler@stat.math.ethz.ch>
1372 :    
1373 :     * R/sparseMatrix.R (prSpMatrix): "." alignment much improved:
1374 :     align with proper position of "0", i.e., right for integers.
1375 :     argument 'align' by default is "fancy".
1376 :    
1377 :     2006-12-14 Martin Maechler <maechler@stat.math.ethz.ch>
1378 :    
1379 :     * R/sparseMatrix.R: delegate "Compare" to "Csparse.."
1380 :     * R/Csparse.R: and fix "Compare" for more cases.
1381 :     * tests/Class+Meth.R: test some of these (m == m, m != m)
1382 :    
1383 :     2006-12-13 Martin Maechler <maechler@stat.math.ethz.ch>
1384 :    
1385 :     * R/lsparseMatrix.R: all() and any() methods
1386 :     * R/ldenseMatrix.R: ditto
1387 :     * NAMESPACE, R/Matrix.R: ditto
1388 :    
1389 :     * man/all-methods.Rd: document them minimally
1390 :    
1391 :     * tests/simple.R: add a few examples for these
1392 :    
1393 : maechler 1696 2006-12-11 Martin Maechler <maechler@stat.math.ethz.ch>
1394 :    
1395 :     * R/Tsparse.R ([): fix long standing typo in symmetric case
1396 :     * man/dsCMatrix-class.Rd: add example exhibiting the above case
1397 :    
1398 : bates 1691 2006-12-10 Douglas Bates <bates@stat.wisc.edu>
1399 :    
1400 :     * src/CHMfactor.c (CHMfactor_to_sparse): change LDL factorization
1401 :     to LL before converting to a sparse matrix. (The LDL form can be
1402 :     converted to a sparse matrix but it is implicitly a unit
1403 :     triangular matrix and a diagonal matrix overwritten on the diagonal.)
1404 :    
1405 :     2006-12-09 Douglas Bates <bates@stat.wisc.edu>
1406 :    
1407 :     * src/chm_common.c (chm_factor_to_SEXP): allocate and fill the Dim slot.
1408 :    
1409 : bates 1688 2006-12-08 Douglas Bates <bates@stat.wisc.edu>
1410 :    
1411 :     * DESCRIPTION (Version): updated -> release 0.9975-7
1412 :     * src/{init.c,chm_common.c}, inst/include/*: export cholmod_analyze_p
1413 :    
1414 : maechler 1682 2006-11-30 Martin Maechler <maechler@stat.math.ethz.ch>
1415 :    
1416 :     * R/diagMatrix.R (%*%): write a direct [diag o Csparse] method
1417 :    
1418 : bates 1681 2006-11-29 Douglas Bates <bates@stat.wisc.edu>
1419 :    
1420 :     * src/dgeMatrix.c (dgeMatrix_solve): Check error code from dgetri.
1421 :     * tests/dg_Matrix.R: Add Barry Rowlingson's test of a matrix that
1422 :     is exactly singular.
1423 :    
1424 : maechler 1674 2006-11-07 Martin Maechler <maechler@stat.math.ethz.ch>
1425 :    
1426 :     * DESCRIPTION (Date): updated -> release 0.9975-6
1427 :    
1428 : maechler 1673 2006-11-06 Martin Maechler <maechler@stat.math.ethz.ch>
1429 :    
1430 :     * R/Csparse.R (replCmat): symmetric indexing of symmetric matrix
1431 :     now returns symmetric.
1432 :    
1433 :     * R/zzz.R ("diag<-"): replace "diag<-" in base for R <= 2.4.x
1434 :    
1435 :     * R/Matrix.R (.M.sub.i.2col): new, for M[ cbind(i,j) ] indexing.
1436 :     * R/Matrix.R (.M.repl.i.2col): new, for M[ cbind(i,j) ] <- value
1437 :    
1438 :     * R/Auxiliaries.R (.type.kind): added
1439 :    
1440 :     2006-11-04 Martin Maechler <maechler@stat.math.ethz.ch>
1441 :    
1442 :     * src/cs.[ch]: updated to CSparse Version 2.0.3 by simply
1443 :     running src/CSparse_install.sh
1444 :    
1445 :     * R/denseMatrix.R: "[": keep symmetric on symmetric indexing.
1446 :    
1447 : maechler 1665 2006-11-03 Martin Maechler <maechler@stat.math.ethz.ch>
1448 :    
1449 :     * src/dsCMatrix.c (dsCMatrix_Csparse_solve): new
1450 :     * R/dsCMatrix.R (solve): "fully-sparse" using the above.
1451 :    
1452 :     * R/AllClass.R: "pMatrix" now also inherits from "generalMatrix"
1453 :    
1454 :     * tests/Class+Meth.R (tstMatrixClass): now assure
1455 :     the (important in method programming) property :
1456 :    
1457 :     ###>> Every "Matrix" is either
1458 :     ###>> "general*", "symmetric*", "triangular*" or "diagonal*"
1459 :    
1460 :     (where "*" stands for "Matrix")
1461 :    
1462 :     * R/Auxiliaries.R (diagU2N): now .Call()s Csparse_diagU2N for <Csparse>
1463 :    
1464 :     * R/dMatrix.R (Compare(<dMatrix>,<dMatrix>): update and
1465 :     * tests/validObj.R: checks for "comparison"
1466 :    
1467 :     * R/sparseMatrix.R ([): improved indexing for sparse;
1468 :     trying to keep <symmetric>[ n, n] symmmetric
1469 :    
1470 :     * tests/indexing.R: indexing for logical sparse now ok
1471 :    
1472 :    
1473 : maechler 1660 2006-11-02 Martin Maechler <maechler@stat.math.ethz.ch>
1474 :    
1475 : maechler 1661 * src/Tsparse.c: use xTsparse_validate() , and hence remove
1476 :    
1477 :     * src/{ltC,lsC,lgT}Matrix.[ch]: removed
1478 :    
1479 :     2006-11-02 Martin Maechler <maechler@stat.math.ethz.ch>
1480 :    
1481 : maechler 1660 * R/AllClass.R (Matrix-class): check length of dimnames in validity.
1482 :    
1483 :     * tests/simple.R: validObject() checking the above.
1484 :    
1485 : maechler 1665 * src/dgCMatrix.c (xCMatrix_validate): new, small and simple,
1486 : maechler 1660 replacing both dgCMatrix_validate and lgCM*.
1487 :    
1488 :     * src/Csparse.c (Csparse_dense_prod, etc): do not lose dimnames;
1489 :     fix dimnames setting in other places.
1490 :     * src/chm_common.c (chm_dense_to_SEXP): now can pass dimnames
1491 :    
1492 : maechler 1659 2006-11-01 Martin Maechler <maechler@stat.math.ethz.ch>
1493 :    
1494 : maechler 1660 * R/Csparse.R,src/Csparse.c, etc: tcrossprod(<CsparseM>,<CsparseM>)
1495 :    
1496 :     * R/sparseMatrix.R (isSymmetric): drop 'factors' slot for
1497 :     symmetry test, via
1498 : maechler 1659 * R/Auxiliaries.R (.as.dgC.0.factors):
1499 :    
1500 : bates 1657 2006-11-01 Douglas Bates <bates@r-project.org>
1501 :    
1502 :     * R/Csparse.R,src/Csparse.c,tests/matprod.R,
1503 :     man/CsparseMatrix-class.Rd: crossprod(<CsparseMatrix>,
1504 :     <CsparseMatrix>) added
1505 :    
1506 : maechler 1655 2006-10-30 Martin Maechler <maechler@stat.math.ethz.ch>
1507 :    
1508 :     * tests/matprod.R: add a variation of Harri's example
1509 :    
1510 :     * R/dsparseMatrix.R: fix crossprod(<dsparse>, <dge>) to *not*
1511 :     recursive infinitely.
1512 :    
1513 :     * R/dgCMatrix.R: + solve(<sparse>, <sparse>)
1514 :    
1515 :     * tests/indexing.R: add test for the "<" bug fixed 10-27 in R/dMatrix.R
1516 :    
1517 :     2006-10-28 Martin Maechler <maechler@stat.math.ethz.ch>
1518 :    
1519 :     * tests/Class+Meth.R (tstMatrixClass): more: use non-trivial
1520 :     matrix if possible; test m+m == 2*m; now test dgRMatrix.
1521 :     * R/dgRMatrix.R (.to.dgR): a few more coercions, in order to
1522 :     satisfy the above test.
1523 :    
1524 : maechler 1654 2006-10-27 Martin Maechler <maechler@stat.math.ethz.ch>
1525 :    
1526 : maechler 1655 * R/Matrix.R (Ops): <Matrix> o <matrix> method added
1527 :    
1528 : maechler 1654 * R/dgCMatrix.R: solve(a, b="missing") based on
1529 :     * src/dgCMatrix.c (dgCMatrix_matrix_solve): extend to work with
1530 :     RHS = NULL.
1531 :    
1532 :     * R/diagMatrix.R (diagdiagprod): extend %*% etc to ldiMatrix;
1533 :     add more (needed) [t]crossprod() methods.
1534 :    
1535 :     * man/ddiMatrix-class.Rd: more info, notably on 'diag'
1536 :    
1537 :     * R/Auxiliaries.R (as_CspClass): cleanup
1538 :     (drop0): internal utility for "Csparse_drop(*, 0)"
1539 :     (.bail.out.2): encourage active feedback
1540 :    
1541 :     2006-10-26 Martin Maechler <maechler@stat.math.ethz.ch>
1542 :    
1543 :     * R/dMatrix.R(Compare): new(), then slots [no validity check]
1544 :    
1545 :     * src/Csparse.c (Csparse_validate): fixed (and more efficient in
1546 :     non-valid or 'sorted' case).
1547 :    
1548 :     * R/dsparseMatrix.R: add "chol" method.
1549 :     * R/ddenseMatrix.R: ditto
1550 :    
1551 :     * R/diagMatrix.R (Ops): group methods for <diagonal> o <sparse>
1552 :     * NAMESPACE (Ops)
1553 :     * R/diagMatrix.R (diag2T): simple utility used "higher level"
1554 :     coercion; deprecating direct lower level coercions.
1555 :    
1556 :     * R/*.R (seq): use seq_len() and seq_along() where possible.
1557 :    
1558 :    
1559 : maechler 1647 2006-10-23 Martin Maechler <maechler@stat.math.ethz.ch>
1560 :    
1561 :     * DESCRIPTION (Version): 0.9975-5 ready for release
1562 :    
1563 : bates 1646 2006-10-20 Douglas Bates <bates@stat.wisc.edu>
1564 :    
1565 :     * src/init.c (R_init_Matrix): export more cholmod CCallable functions.
1566 :    
1567 : maechler 1642 2006-10-20 Martin Maechler <maechler@stat.math.ethz.ch>
1568 :    
1569 :     * R/AllClass.R (corMatrix): add 'validity' check;
1570 :     comment out unused "LDL" class definition
1571 :     * NAMESPACE: mention, but do not export "LDL" class
1572 :     * R/corMatrix.R: new (simple), needed for R-devel with
1573 :     * tests/Class+Meth.R (tstMatrixClass): 1 exception for corMatrix
1574 :     coerce and t() exceptions for all 5 'Mat.MatFact' classes.
1575 :    
1576 : bates 1641 2006-10-19 Douglas Bates <bates@stat.wisc.edu>
1577 :    
1578 :     * src/chm_common.h: Add R_cholmod_start to initialize cholmod to
1579 :     use Rprintf and R's error handling.
1580 :    
1581 : maechler 1635 2006-10-17 Martin Maechler <maechler@stat.math.ethz.ch>
1582 :    
1583 :     * R/diagMatrix.R (%*%): rep(*, each = .) in Matrix %*% diagonal.
1584 :     * tests/matprod.R: add tests for the bug fixed.
1585 :    
1586 : bates 1624 2006-10-11 Douglas Bates <bates@stat.wisc.edu>
1587 :    
1588 :     * src/HBMM.[ch]: remove HarwellBoeing format for writing.
1589 :     * src/SOURCES_C.mkf (SOURCES_C): no longer compile iohb.c
1590 :    
1591 :     2006-10-06 Douglas Bates <bates@stat.wisc.edu>
1592 :    
1593 : bates 1629 * R/d[gs]CMatrix.R: deprecate the writeHB function. Use writeMM instead.
1594 : bates 1624
1595 : maechler 1618 2006-10-06 Martin Maechler <maechler@stat.math.ethz.ch>
1596 :    
1597 :     * DESCRIPTION (Version): 0.9975-3
1598 :    
1599 :     * R/diagMatrix.R (bdiag): new function constructing block diagonal
1600 :     (sparse) matrices.
1601 :     * man/bdiag.Rd: docu + examples
1602 :    
1603 : maechler 1619 * R/Csparse.R (replCmat): calling new Csparse_drop() now.
1604 :    
1605 : maechler 1618 * src/Csparse.c (Csparse_general_to_symmetric, Csparse_drop): new functions
1606 :     * R/lsCMatrix.R: three more coercions to lsC (thanks to the above)
1607 :    
1608 :     * R/diagMatrix.R (Diagonal): '[<-' method for diag.matrices such
1609 :     that result is sparse or diagonal (and not dense).
1610 :    
1611 :     * man/Subassign-methods.Rd: fix examples
1612 :    
1613 :     * R/Matrix.R (Matrix): Matrix(0, *) or Matrix(*, sparse=TRUE)
1614 :     should always return a sparse (and not sometimes a diagonal) matrix.
1615 :    
1616 : maechler 1615 2006-10-05 Martin Maechler <maechler@stat.math.ethz.ch>
1617 :    
1618 :     * R/Matrix.R ([<-): also for value "Matrix" or "matrix"
1619 :    
1620 : bates 1613 2006-10-04 Douglas Bates <bates@stat.wisc.edu>
1621 :    
1622 :     * DESCRIPTION (Version): 0.9975-2
1623 : maechler 1615
1624 : bates 1613 * inst/include/Matrix_stubs.c (M_cholmod_sparse_to_triplet): export more symbols
1625 :    
1626 : bates 1611 2006-10-02 Douglas Bates <bates@R-project.org>
1627 :    
1628 :     * tests/dg_Matrix.R: Simplify test taking into account new code.
1629 :    
1630 : maechler 1599 2006-09-29 Martin Maechler <maechler@stat.math.ethz.ch>
1631 :    
1632 : maechler 1600 * R/Csparse.R (replCmat): improve for missing i / j in non-simple cases
1633 :    
1634 : maechler 1599 * R/lsTMatrix.R: new files w/ missing methods
1635 :     * R/nsTMatrix.R: " 'for completeness'
1636 :    
1637 :     * tests/Class+Meth.R: a bit less 'not.ok.classes'
1638 :    
1639 :     * R/Tsparse.R (t): generalized "t" method from "dgT*" to "Tsparse*"
1640 :    
1641 :    
1642 : bates 1595 2006-09-28 Douglas Bates <bates@R-project.org>
1643 :    
1644 :     * src/dppMatrix.h: Ensure definition of dspMatrix_validate is
1645 :     included.
1646 :    
1647 :     * src/init.c, inst/include/{Matrix.h,Matrix_stubs.h,cholmod.h}:
1648 :     Export C-callable functions used in Zt_create in lme4.
1649 :    
1650 : maechler 1592 2006-09-28 Martin Maechler <maechler@stat.math.ethz.ch>
1651 :    
1652 :     * DESCRIPTION (Version): 0.9975-1
1653 :    
1654 :     * tests/simple.R: less checks fail; using NA, found that our
1655 :     kronecker() is not base-compatible with NA's.
1656 :    
1657 :     * R/dMatrix.R: "Compare" method now implemented for all cases
1658 :    
1659 :     * R/Auxiliaries.R (indTri): == which([lower/upper].tri( * )) new utility
1660 :    
1661 :     * man/dtpMatrix-class.Rd: mention length of 'x' slot
1662 :    
1663 :     * src/dtpMatrix.c (dtpMatrix_validate): fix check
1664 :     * src/dspMatrix.c (dspMatrix_validate): ditto
1665 :    
1666 :     * R/dtTMatrix.R (gt2tT): fix ("l" -> "n")
1667 :     including coercion to [nl]tTMatrix.
1668 :    
1669 :     * R/diagMatrix.R (show): print a header line as for other classes.
1670 :    
1671 :     2006-09-27 Martin Maechler <maechler@stat.math.ethz.ch>
1672 :    
1673 :     * src/Makefile.win (SUBDIRS): fix typo
1674 :    
1675 : maechler 1583 2006-09-19 Martin Maechler <maechler@stat.math.ethz.ch>
1676 :    
1677 :     * DESCRIPTION (Date): ready to release 0.9975-0 to CRAN
1678 :    
1679 : bates 1577 2006-09-18 Douglas Bates <bates@stat.wisc.edu>
1680 :    
1681 :     * R/[CT]sparse.R (crossprod and tcrossprod): Handle the cases for x
1682 :     symmetric and y missing in R code using %*% (cholmod_aat doesn't
1683 :     accept a symmetric matrix).
1684 :     * tests/group-methods.R: Uncomment test of crossprod applied to
1685 :     lsCMatrix objects.
1686 :    
1687 : maechler 1575 2006-09-18 Martin Maechler <maechler@stat.math.ethz.ch>
1688 :    
1689 :     * R/AllClass.R (symmetricMatrix): add validity method (available
1690 :     in C for a long time). Many "n..Matrix": drop (wrong) validity arg.
1691 :    
1692 :     * src/lgCMatrix.c (lgCMatrix_validate): check 'x' slot (!)
1693 :    
1694 :     * tests/indexing.Rout.save:
1695 :     * tests/indexing.R: additions, mainly for 'lsparse'
1696 :    
1697 :     * R/diagMatrix.R (Diagonal) & coercion to lgTMatrix: fixes for NA
1698 :     case.
1699 :    
1700 :     * R/Auxiliaries.R (nz.NA): new utility now used in nnzero()
1701 :    
1702 : maechler 1571 2006-09-16 Martin Maechler <maechler@stat.math.ethz.ch>
1703 :    
1704 : maechler 1572 * R/sparseMatrix.R (prSpMatrix): print logical NAs "visibly"
1705 :     as 'N' (1-letter - Ok?)
1706 :    
1707 : maechler 1571 * tests/group-methods.R: add test for logical + NAs
1708 :    
1709 :     * R/dMatrix.R ("Compare"): fix to work with NA's
1710 :    
1711 :     * R/AllClass.R: "Cholesky" etc now inherit from MatrixFactorization.
1712 :    
1713 :     * src/lgCMatrix.c (ncsc_to_matrix): renamed from lcsc_to_matrix()
1714 :     which is implemented.
1715 :    
1716 : maechler 1565 2006-09-15 Martin Maechler <maechler@stat.math.ethz.ch>
1717 :    
1718 : maechler 1571 * src/chm_common.c: coerce logical <-> double instead of
1719 :     typecasting; needed for "l" matrix handling in cholmod.
1720 : maechler 1565
1721 : maechler 1571 * tests/other-pkgs.R (graph): small extension in "graph" checks.
1722 :    
1723 : maechler 1565 * R/sparseMatrix.R (graphNEL -> Tsparse): method for weight case.
1724 :     (Tsp2grNEL): other fixes needed
1725 :    
1726 : maechler 1548 2006-09-11 Martin Maechler <maechler@stat.math.ethz.ch>
1727 :    
1728 :     * R/AllClass.R ("nMatrix"): and subclasses for "nonzero pattern"
1729 :     Matrices, since "lMatrix", also "lsparseM" can have NA
1730 :     * R/ndenseMatrix.R, etc: new source files
1731 :     * man/nsparseMatrix-classes.Rd, etc: new help files
1732 :     * tests/: adaptions
1733 :     * src/chm_common.c (chm_dense_to_SEXP): and others:
1734 :     new 'Rkind' argument: "l*" and "d*" both use CHOLMOD_REAL
1735 : maechler 1582 * src/Csparse.c, etc: ditto
1736 : maechler 1548
1737 : bates 1546 2006-09-11 Douglas Bates <bates@R-project.org>
1738 :    
1739 :     * src/Mutils.[ch],init.c inst/include/*.h: Move the
1740 :     alloc_d**Matrix functions to the lme4 package.
1741 :    
1742 : bates 1543 2006-09-09 Douglas Bates <bates@R-project.org>
1743 :    
1744 :     * src/dsCMatrix.c (dsCMatrix_Cholesky): igoring LDL = FALSE now
1745 : maechler 1544 fixed
1746 : bates 1543
1747 : maechler 1544 2006-09-09 Martin Maechler <maechler@stat.math.ethz.ch>
1748 :    
1749 : maechler 1548 * R/lMatrix.R: new
1750 :    
1751 : maechler 1544 * R/sparseMatrix.R (Tsp2grNEL): do not yet use graph::foo()
1752 :    
1753 :     * R/dgeMatrix.R: do not define tcrossprod() methods for "matrix"
1754 : maechler 1582 * man/tcrossprod.Rd: ditto
1755 : maechler 1544
1756 : bates 1538 2006-09-08 Douglas Bates <bates@stat.wisc.edu>
1757 :    
1758 :     * inst/include/Matrix_stubs.c,Matrix.h: Add declarations and stubs
1759 :     for exported functions
1760 :     * src/Makefile, src/CHOLMOD/Lib/Makefile, src/Metis,CAMD,CCOLAMD:
1761 :     Remove partitioning algorithms for sparse matrix reordering. The
1762 :     copyright on the Metis code was problematic and the methods were
1763 :     rarely used.
1764 :     * src/triplet_to_col.[ch],MMHB.[ch]: Remove triplet_to_col. Such
1765 :     operations are now done entirely in CHOLMOD code.
1766 :    
1767 : bates 1517 2006-09-06 Douglas Bates <bates@R-project.org>
1768 :    
1769 :     * src/Mutils.h: Remove functions that are no longer used.
1770 :    
1771 : bates 1507 2006-09-04 Douglas Bates <bates@R-project.org>
1772 :    
1773 :     * src/dtCMatrix.c (dtCMatrix_validate): rename functions.
1774 :     * src/DEPS.mkf: update
1775 :    
1776 : maechler 1481 2006-09-02 Martin Maechler <maechler@stat.math.ethz.ch>
1777 :    
1778 :     * created branches/Matrix-for-R-2.3.x; on trunk: do
1779 :     * DESCRIPTION (Version): 0.9975-0
1780 :     (Depends): R (>= 2.4.0)
1781 :    
1782 : bates 1475 2006-09-01 Douglas Bates <bates@R-project.org>
1783 :    
1784 :     * R/sparseMatrix.R: Added direct method to CsparseMatrix from graphNEL
1785 :    
1786 : maechler 1472 2006-09-01 Martin Maechler <maechler@stat.math.ethz.ch>
1787 :    
1788 :     * R/sparseMatrix.R: add coercion from "ANY" to "sparseMatrix"
1789 :     * R/denseMatrix.R: add coercion from "ANY" to "denseMatrix"
1790 :    
1791 :     * R/Matrix.R ([): use nargs() to disambiguate M[i] and M[i,]
1792 :    
1793 :     2006-08-31 Martin Maechler <maechler@stat.math.ethz.ch>
1794 :    
1795 :     * R/sparseMatrix.R (Arith): moved Arith group method one-level up
1796 :     from "dsparse" to "sparse" and now go via "Csparse" instead of "dgC"
1797 : maechler 1582 * R/dsparseMatrix.R: ditto
1798 :     * R/Csparse.R: ditto
1799 : maechler 1472
1800 :     2006-08-31 Martin Maechler <maechler@stat.math.ethz.ch>
1801 :    
1802 :     * R/dMatrix.R (Compare): improve availability of "<", etc
1803 :     * R/Auxiliaries.R (asTuniq): new; also make use of R 2.4.x print(*,max)
1804 :    
1805 : maechler 1467 2006-08-30 Martin Maechler <maechler@stat.math.ethz.ch>
1806 :    
1807 :     * R/dgCMatrix.R: aargh: "Arith(<dgC>, numeric)" was wrong because
1808 :     of a 0-index which was used as 1-index (..hmm)
1809 :    
1810 :     * R/sparseMatrix.R (prSpMatrix): fix printing an all-0 sparse Matrix
1811 :    
1812 :     * R/Auxiliaries.R (all0, is0): for 0-testing in presence of NA's
1813 :     * R/Auxiliaries.R (isTriMat): use all0() for 0-testing.
1814 : maechler 1582 (.is.diagonal): ditto
1815 : maechler 1467
1816 :     * R/lgTMatrix.R: as("matrix", "lgTMatrix"): warn about NA's
1817 :    
1818 :     * R/Matrix.R (Matrix): also work for NA data
1819 :    
1820 : maechler 1455 2006-08-28 Martin Maechler <maechler@stat.math.ethz.ch>
1821 :    
1822 :     * R/Matrix.R (Matrix): + 'forceCheck' argument; dimnames setting
1823 :     in all cases.
1824 :    
1825 : bates 1453 2006-08-27 Douglas Bates <bates@R-project.org>
1826 :    
1827 :     * src/dense.[ch],init.c, R/ddenseMatrix.R, man/band.Rd
1828 :     (ddense_band): Added triu, tril and band for ddenseMatrix objects.
1829 :    
1830 : maechler 1447 2006-08-25 Martin Maechler <maechler@stat.math.ethz.ch>
1831 :    
1832 :     * src/Mutils.c (dup_mMatrix_as_dgeMatrix): added all subclasses of
1833 :     subclasses of "ddenseMatrix"
1834 :     * src/init.c et al: outcomment dtrM*_as_dge* and dsyM*_as_dge*_
1835 :     * R/ddenseMatrix.R et al: setAs("ddenseMatrix", "dgeMatrix", ..)
1836 :     instead of half dozen specialized ones.
1837 :    
1838 : bates 1445 2006-08-25 Douglas Bates <bates@R-project.org>
1839 :    
1840 :     * R/lmer.R (qqmath method): Bug fix provided by Emmanuel Tillard
1841 :     <tillard@cirad.fr> - ordering standard errors to match effects.
1842 :    
1843 : bates 1439 2006-08-24 Douglas Bates <bates@R-project.org>
1844 : bates 1431
1845 : bates 1439 * src/lsCMatrix.c (lsCMatrix_trans): Remove lsCMatrix_chol based
1846 :     on R_ldl.
1847 :     * R/lCholCMatrix.R,
1848 :     src/[dl]CholCMatrix.[ch],R_ldl.[ch],Metis_utils.[ch]: removed
1849 :     * src/dsCMatrix.c (dsCMatrix_to_dgTMatrix): use CHOLMOD
1850 :     * many files in ./R and ./src: Use more general version of
1851 :     dup_mMatrix_as_dgeMatrix to simplify method definitions.
1852 : bates 1442 * src/Mutils.c (dup_mMatrix_as_dgeMatrix): Add ddiMatrix,
1853 :     dtpMatrix, dspMatrix and dppMatrix conversions.
1854 :    
1855 : maechler 1447
1856 : bates 1439 2006-08-23 Douglas Bates <bates@R-project.org>
1857 :    
1858 :     * R/AllClass.R,lCholCMatrix.R,src/SOURCES_C.mkf,init.c,NAMESPACE:
1859 :     Remove classes lCholCMatrix and dCholCMatrix based on R_ldl code.
1860 : bates 1431 * src/dgeMatrix.c: Ensure 'factors' slot exists in result of
1861 :     dgeMatrix_crossprod (may need to do this in other places).
1862 :     * R/AllGeneric.R,dsCMatrix.R, src/dscMatrix.[ch]: Add Cholesky
1863 :     generic and method for dsCMatrix. Use CHOLMOD for chol().
1864 :    
1865 : bates 1414 2006-08-22 Douglas Bates <bates@R-project.org>
1866 :    
1867 :     * src/Mutils.c (dup_mMatrix_as_dgeMatrix): updated for general
1868 :     types of classed Matrices, matrices or numeric or logical vectors.
1869 : bates 1423 * src/init.c: register dup_mMatrix_as_dgeMatrix for coercions.
1870 :     * src/chm_common.c,Mutils.h (as_cholmod_factor): Move check_class
1871 :     to Mutils.h (as an inline) and change name to Matrix_check_class;
1872 :     fixes in as_cholmod_factor and chm_factor_to_SEXP.
1873 :     * src/dsCMatrix.[ch]: Use CHOLMOD for dsCMatrix_chol and
1874 :     dsCMatrix_matrix_solve. Comment out vestigial functions.
1875 :     * src/Csparse.c: use diag_P and uplo_P macros.
1876 : maechler 1447
1877 : bates 1405 2006-08-21 Douglas Bates <bates@R-project.org>
1878 :    
1879 :     * src/lmer.c (internal_mer_RZXinv): Fix memory leak caught by
1880 : maechler 1447 valgrind.
1881 : bates 1411 * tests/matprod.R: Add tests to verify that 'solve' and '%*%' are
1882 :     inverses.
1883 :     * src/sparseQR.c (sparseQR_validate): add new validation test, fix
1884 :     -Wall warnings.
1885 :     * src/dppMatrix.c,dtrMatrix.c,dgCMatrix.c,dgeMatrix.c,dspMatrix.c:
1886 :     Use dup_mMatrix_as_dgeMatrix.
1887 : maechler 1447
1888 : bates 1403 2006-08-20 Douglas Bates <bates@R-project.org>
1889 :    
1890 :     * src/sparseQR.c: Fix thinko in sparseQR_resid_fitted.
1891 :     * tests/sparseQR.R: Added
1892 :     * man/sparseQR-class.Rd: Document methods for qr.* generics
1893 :     * R/sparseQR.R: Return correct # of coefs; fix cut-and-paste errors
1894 :    
1895 : bates 1398 2006-08-19 Douglas Bates <bates@R-project.org>
1896 :    
1897 :     * NAMESPACE, R/sparseQR.R, src/init.c,sparseQR.[ch],SOURCES_C.mkf:
1898 :     Added methods for sparseQR for qr.qy, qr.qty, qr.coef, qr.resid
1899 :     and qr.fitted.
1900 :     * src/Mutils.[ch]: Added dup_mMatrix_as_dgeMatrix utility
1901 :     * src/dgCMatrix.c: Check for ordering before storing q in dgCMatrix_QR
1902 :    
1903 : maechler 1389 2006-08-18 Martin Maechler <maechler@stat.math.ethz.ch>
1904 :    
1905 :     * R/AllGeneric.R: add "qr" and "chol" generics; via 'trick' since
1906 :     the base version has no "..." argument.
1907 :    
1908 :     * R/sparseMatrix.R (prSpMatrix): fix the triangular unit diagonal case.
1909 :    
1910 :     * R/Matrix.R: define and
1911 :     * NAMESPACE: export as.numeric() and as.logical() methods.
1912 :     Let's hope these do not badly slow down something...
1913 :     Finally export the zapsmall() method.
1914 :    
1915 : bates 1388 2006-08-17 Douglas Bates <bates@R-project.org>
1916 :    
1917 :     * src/dgCMatrix.[ch] (dgCMatrix_matrix_solve), src/init.c,
1918 :     R/dgCMatrix.R: solve methods for dgCMatrix and dense RHS.
1919 :     * src/dtCMatrix.c :Remove code that is no longer used
1920 :     * R/dtCMatrix.R: Use C code for diagU2N in CsparseMatrix classes
1921 :    
1922 : bates 1370 2006-08-14 Douglas Bates <bates@R-project.org>
1923 :    
1924 : bates 1373 * src/Csparse.[ch],init.c (Csparse_to_logical): Added utilities
1925 :     Csparse_to_logical and Csparse_symmetric_to_general.
1926 :     * R/dgCMatrix.R,dsCMatrix.R,Csparse.R : Consolidate general
1927 : maechler 1389 coercion methods between CsparseMatrix and TsparseMatrix.
1928 : bates 1373
1929 :     2006-08-14 Douglas Bates <bates@R-project.org>
1930 :    
1931 : bates 1370 * R/dtCMatrix.R,dgCMatrix.R,Csparse.R src/init.c,dgCMatrix.[ch],
1932 :     Csparse.[ch],chm_common.c,dense.c : Use CHOLMOD code and methods
1933 :     for CsparseMatrix, TsparseMatrix, denseMatrix or matrix when
1934 :     possible.
1935 :    
1936 : bates 1368 2006-08-12 Douglas Bates <bates@R-project.org>
1937 :    
1938 :     * src/chm_common.[ch],Csparse.[ch],Tsparse.[ch],CHMfactor.c,dtTMatrix.c,
1939 :     dgTMatrix.c,dgCMatrix.c,dsCMatrix.c,dtTMatrix.c, R/dsTMatrix.R,
1940 :     Tsparse.R,Csparse.R,dgTMatrix.R,dsCMatrix.R,lsCMatrix.R:
1941 :     generalize conversions between TsparseMatrix, CsparseMatrix,
1942 :     denseMatrix and matrix. Preserve triangularity property and
1943 :     propagate Dimnames in the easy cases.
1944 :    
1945 : bates 1365 2006-08-10 Douglas Bates <bates@R-project.org>
1946 :    
1947 :     * src/lmer.c: adjust checks in glmer_init for S4SXP
1948 :     * tests/validObj.R: check of all(eq) should be all(eq@x) - worked
1949 :     before S4SXP but for the wrong reasons.
1950 :    
1951 : bates 1354 2006-08-08 Douglas Bates <bates@R-project.org>
1952 :    
1953 : bates 1360 * src/Csparse.c (Csparse_crossprod): tcrossprod result has stype = -1.
1954 :     Later modified to return the upper triangle only.
1955 :     * R/dgTMatrix.R: Remove vestigial crossprod and tcrossprod methods.
1956 : maechler 1389
1957 : bates 1352 2006-08-07 Douglas Bates <bates@R-project.org>
1958 :    
1959 :     * src/Csparse.c (Csparse_crossprod): Set stype on result to avoid
1960 :     R-level conversion to a sparse symmetric class.
1961 :     * R/Tsparse.R,R/Csparse.R (crossprod and tcrossprod methods):
1962 :     Remove conversion to sparse symmetric classes (now done in C code).
1963 :    
1964 : maechler 1349 2006-08-07 Martin Maechler <maechler@stat.math.ethz.ch>
1965 :    
1966 : maechler 1351 * R/dgCMatrix.R: disable old crossprod and tcrossprod methods
1967 :     * man/band.Rd: adapt the \dontshow{} unit test.
1968 :    
1969 :     2006-08-07 Martin Maechler <maechler@stat.math.ethz.ch>
1970 :    
1971 : maechler 1349 * DESCRIPTION (Version): 0.995-14 for CRAN
1972 :    
1973 :     * tests/other-pkgs.R: oops: library(Matrix) outside *if* !
1974 :    
1975 :     * R/sparseMatrix.R (Tsp2grNEL): fixed Tsparse -> graph coercion
1976 :     * tests/other-pkgs.R: more checks, sparseMatrix -> graph
1977 :    
1978 :     * R/Auxiliaries.R (as_Tsparse, as_Rsparse): new
1979 :     * R/Tsparse.R (tril, triu, band): methods
1980 : bates 1352 * R/dgRMatrix.R (tril, ...): ditto
1981 :     * man/band.Rd: ditto
1982 : maechler 1349
1983 :     2006-08-04 Martin Maechler <maechler@stat.math.ethz.ch>
1984 :    
1985 :     * R/Matrix.R (head, tail): directly use utils:::head.matrix
1986 :     to be up-to-date automatically.
1987 :    
1988 : maechler 1346 2006-08-03 Martin Maechler <maechler@stat.math.ethz.ch>
1989 :    
1990 :     * DESCRIPTION (Version): 0.995-13 to be released to CRAN
1991 :    
1992 :     * DESCRIPTION (Lazydata): no, instead of 'yes' because it fails for:
1993 :     * data/CAex.R, inst/external/CAex_slots.rda: replacing data/CAex.rda
1994 :     * data/KNex.R, inst/external/KNex_slots.rda: replacing data/KNex.rda
1995 :     such that the S4 objects are always created by the current version
1996 :     of R and 'Matrix' class definitions.
1997 :    
1998 : bates 1342 2006-08-01 Douglas Bates <bates@R-project.org>
1999 :    
2000 :     * R/lmer.R (LMEoptimize method), tests/lmer.R,
2001 : maechler 1346 inst/external/test3comp.rda: Added warnings for convergence on
2002 : bates 1342 boundary and test cases.
2003 :    
2004 :     * src/lmer.c (mer_postVar): Modified to return the variances that
2005 :     are marginal to the fixed effects, not conditional on them (which
2006 :     is what the bVar slot contents represent).
2007 :    
2008 : bates 1338 2006-07-31 Douglas Bates <bates@R-project.org>
2009 :    
2010 :     * NAMESPACE, src/lmer.c, R/lmer.R (hatTrace): Add the hatTrace
2011 :     function which calls the C function mer_hat_trace2.
2012 : maechler 1346
2013 : bates 1342 * man/ranef.Rd: Include description of "postVar" argument and
2014 :     producing a caterpillar plot.
2015 : bates 1338
2016 : maechler 1335 2006-07-31 Martin Maechler <maechler@stat.math.ethz.ch>
2017 :    
2018 :     * NAMESPACE: change "correlation" to "corMatrix"
2019 :     * R/AllClass.R: to avoid clash with S3 class in 'nlme'.
2020 : bates 1352 * R/dpoMatrix.R: ditto
2021 :     * R/lmer.R: ditto
2022 : maechler 1335
2023 : bates 1338 2006-07-28 Douglas Bates <bates@R-project.org>
2024 :    
2025 :     * src/lmer.c (internal_mer_RZXinv): Split the calculation of the
2026 :     RZXinv slot's contents into a separate internal function that can
2027 :     be used in mer_hat_trace.
2028 :    
2029 : maechler 1331 2006-07-22 Martin Maechler <maechler@stat.math.ethz.ch>
2030 :    
2031 :     * R/Matrix.R: Coercions "Matrix" -> (sparse|dense)Matrix
2032 :     via new smart
2033 :     * R/Auxiliaries.R (as_Csparse, as_dense, .M.shapse): new
2034 :     utility functions.
2035 :    
2036 :    
2037 : maechler 1330 2006-07-21 Martin Maechler <maechler@stat.math.ethz.ch>
2038 :    
2039 : maechler 1331 * R/Csparse.R (tril, triu, band): do return *triangular* classed
2040 :     matrices when appropriate; band() even symmetric ones.
2041 :     (replCmat): extend to potentially all "CsparseMatrix"
2042 :     * R/Tsparse.R (replTmat): extend to all "TsparseMatrix"; hence
2043 :     allow subassignment for special sparse matrices.
2044 :    
2045 :     * R/Auxiliaries.R (as_geClass): factor out the .M.kind() functionality
2046 :    
2047 : maechler 1330 * src/lmer.c (mer_MCMCsamp, glmer_MCMCsamp): new 'verbose'
2048 :     argument; in glmer_*(): print only if(verbose).
2049 :    
2050 :     speed-optimize a few places by moving REAL(.) out of loops.
2051 :    
2052 :     * src/lmer.h, src/init.h, R/lmer.R: related to above.
2053 :    
2054 : maechler 1329 2006-07-20 Martin Maechler <maechler@stat.math.ethz.ch>
2055 :    
2056 :     * R/Matrix.R("["): disable ("Matrix", i = "logical", j = "missing"),
2057 :     since that wrongly triggers also for M[ logi , ]
2058 :    
2059 :     * R/denseMatrix.R: "[" methods now also work e.g. when indexing
2060 :     a symmetric matrix that results in a non-symmetric one.
2061 :     * R/Auxiliaries.R (as_geClass): new function used in "[" above.
2062 :    
2063 :     * R/dMatrix.R: make round(M) work as round(M, 0)
2064 :    
2065 :     * R/dgTMatrix.R (image): coordinate system and axis now use
2066 :     1-based indices, not 0-based ones.
2067 :    
2068 :     * R/Tsparse.R (.ind.prep for "["): get rid of max(<empty>) warning.
2069 :     * tests/indexing.R: test it.
2070 :    
2071 :     * NAMESPACE: export isSymmetric(); has been a generic in "base" for a while;
2072 :     * man/isSymmetric-methods.Rd: and document it.
2073 :    
2074 :     * R/SparseM-conv.R: added coercion methods for some 'SparseM' matrices.
2075 :     * man/SparseM-conv.Rd: docu them
2076 :    
2077 :     * tests/other-pkgs.R: renamed from tests/graph.R and add example
2078 :     for 'SparseM' conversions
2079 :    
2080 :     2006-07-17 Douglas Bates <Douglas.Bates@R-project.org>
2081 :    
2082 :     * R/Matrix.R (head): added head() and tail() methods.
2083 :    
2084 :     2006-07-17 Martin Maechler <maechler@stat.math.ethz.ch>
2085 :    
2086 :     * DESCRIPTION (Version): 0.995-12 released to CRAN
2087 :    
2088 : maechler 1319 2006-07-15 Martin Maechler <maechler@stat.math.ethz.ch>
2089 :    
2090 :     * tests/simple.R: add check for correct dsT -> dgT coercion;
2091 :     add check for correct printing of symmetric sparse matrices.
2092 :    
2093 :     * R/Auxiliaries.R (non0ind): return *all* non-0 entry indices also
2094 :     for sparse symmetric matrices.
2095 :    
2096 :     * src/dsTMatrix.c (dsTMatrix_as_dgTMatrix): do not copy the
2097 :     diagonal twice.
2098 :    
2099 : bates 1316 2006-07-11 Douglas Bates <Douglas.Bates@R-project.org>
2100 :    
2101 :     * src/dsTMatrix.c (dsTMatrix_as_dgTMatrix): Fix a case of INTEGER
2102 : maechler 1319 being applied to the x slot (detected by Brian Ripley).
2103 : bates 1316
2104 : maechler 1315 2006-07-10 Martin Maechler <maechler@stat.math.ethz.ch>
2105 :    
2106 :     * src/dgCMatrix.c (dgCMatrix_validate): 'p' slot must have correct length.
2107 :    
2108 :     * R/Auxiliaries.R (isTriC): fix buglet (we were 1-based!)
2109 :    
2110 :     2006-07-08 Martin Maechler <maechler@stat.math.ethz.ch>
2111 :    
2112 :     * src/lgCMatrix.c (lgCMatrix_diag): new function
2113 :     * R/lgCMatrix.R (diag): for new method
2114 :    
2115 :     * R/AllClass.R (TsparseMatrix): do use Tsparse_validate
2116 :     ==> construction of illegal "*gTMatrix" via new() should
2117 :     now be much less easy:
2118 :     * tests/Class+Meth.R: assertError() for some illegal "dgT*"
2119 :    
2120 :     * R/Matrix.R (Matrix): Matrix(0, nrow,ncol) now "goes sparse"
2121 :     directly.
2122 :     * man/Matrix.Rd: documents it.
2123 :    
2124 : bates 1311 2006-07-06 Douglas Bates <bates@R-project.org>
2125 :    
2126 :     * src/pedigree.c (pedigree_inbreeding): Correction in
2127 :     initialization. This function is not currently being used and is
2128 :     not fully tested.
2129 :    
2130 : bates 1312 * NAMESPACE, R/{AllClass.R,lmer.R}, src/{init.c,lmer.c}:
2131 :     Introduced the glmer class. Added code for mcmcmsamp on glmer
2132 :     objects. Modified validity check on pedigree objects to account
2133 :     for nonparallel patterns of missingness of parents.
2134 : bates 1311
2135 : bates 1313 * man/{lmer-class.Rd,mcmcsamp.Rd}: Update documentation for glmer
2136 :     class.
2137 : maechler 1315
2138 :     2006-07-01 Martin Maechler <maechler@stat.math.ethz.ch>
2139 :    
2140 :     * R/pMatrix.R: coercion pMatrix -> Tsparse
2141 :    
2142 : bates 1300 2006-06-12 Douglas Bates <bates@R-project.org>
2143 :    
2144 : maechler 1319 * DESCRIPTION (Version): 0.995-11 released to CRAN
2145 :    
2146 : bates 1300 * R/lmer.R (mcmcsamp method): Corrected arrangments of names on
2147 :     the output from mcmcsamp.
2148 :    
2149 : bates 1298 2006-06-10 Douglas Bates <bates@R-project.org>
2150 :    
2151 : bates 1300 * R/lmer.R (simulestimate): added C code for calculating the trace
2152 :     of the hat matrix.
2153 : bates 1298
2154 : maechler 1295 2006-06-09 Martin Maechler <maechler@stat.math.ethz.ch>
2155 :    
2156 :     * R/diagMatrix.R (setAs): define coercion methods to sparse matrix
2157 :     classes.
2158 : maechler 1315 * R/sparseMatrix.R etc: multiplication of diagonal and sparse
2159 : maechler 1295
2160 : maechler 1290 2006-06-08 Martin Maechler <maechler@stat.math.ethz.ch>
2161 :    
2162 :     * R/dgTMatrix.R (colSums): etc. All four of
2163 :     colSums(), rowSums(), colMeans(), rowMeans() now should work for
2164 :     all "Matrices".
2165 :    
2166 : bates 1288 2006-06-01 Douglas Bates <bates@stat.wisc.edu>
2167 :    
2168 :     * R/lmer.R (panel.ci): Add a reference line at zero and a
2169 :     background grid to the qqmath plot of ranef.lmer.
2170 :    
2171 : bates 1287 2006-05-30 Douglas Bates <bates@stat.wisc.edu>
2172 : bates 1284
2173 : bates 1287 * R/lmer.R (expandSlash): Functions (non-exported) to allow nested
2174 :     grouping factors to be specified in the formula as (1|foo/bar).
2175 :    
2176 :     2006-05-27 Douglas Bates <bates@stat.wisc.edu>
2177 :    
2178 : bates 1284 * R/lmer.R (findbars and others): Change check of is.numeric to
2179 :     !is.language to resolve the bug reported by Jacob Wegelin.
2180 :    
2181 :     * src/pedigree.c (pedigree_inbreeding): Initial implementation of
2182 :     code to evaluate inbreeding coefficients without calculating T,
2183 :     based on code in Sargolzaei and Iwaisaki's paper.
2184 :    
2185 : bates 1283 2006-05-27 Douglas Bates <bates@stat.wisc.edu>
2186 :    
2187 :     * R/{lmer.R,AllGeneric.R}, src/{init.c,lmer.[ch]}: Added local
2188 :     generic and mer methods for isNested and denomDF. This denomDF was
2189 :     an attempt to emulate that in lme but I don't think that makes
2190 :     sense. Use the trace of the hat matrix instead.
2191 :    
2192 : maechler 1271 2006-05-17 Martin Maechler <maechler@stat.math.ethz.ch>
2193 :    
2194 :     * R/sparseMatrix.R: Matrix <-> graph methods: can no longer use
2195 :     the C code depending on a slot structure that's no longer valid.
2196 : bates 1352 * src/dgTMatrix.c: ditto (also: src/init.c src/dgTMatrix.h)
2197 : maechler 1271
2198 :    
2199 : bates 1268 2006-05-17 Douglas Bates <bates@stat.wisc.edu>
2200 :    
2201 :     * R/{AllGeneric.R,Csparse.R},man/band.Rd,NAMESPACE: changed name
2202 :     of lowerTriMatrix generic and methods to tril (also upper to triu)
2203 :     and added a general band extractor.
2204 :    
2205 : bates 1267 2006-05-16 Douglas Bates <bates@stat.wisc.edu>
2206 :    
2207 :     * R/pedigree.R (pedigree): Replace sire and dam values outside the
2208 :     allowable range with NAs. Added a corresponding check in the
2209 :     validity check for the pedigree class.
2210 :    
2211 :     * R/[CT]sparse.R ([t]crossprod): The result of single-argument
2212 :     crossprod methods now inherits from symmetricMatrix.
2213 :    
2214 : bates 1265 2006-05-15 Douglas Bates <bates@stat.wisc.edu>
2215 :    
2216 :     * R/AllGeneric.R (lowerTriMatrix): Added (but did not export)
2217 :     generics lowerTriMatrix and upperTriMatrix along with methods for
2218 :     the Csparse virtual class. Also added a C function Csparse_band
2219 :     that implements these methods by calling cholmod_band.
2220 :    
2221 : maechler 1264 2006-05-15 Martin Maechler <maechler@stat.math.ethz.ch>
2222 :    
2223 :     * R/Tsparse.R ("["): column or row subsetting; @Dimnames[k] got
2224 :     erased when it was NULL. This led to invalid subselections!
2225 :    
2226 : bates 1259 2006-04-25 Douglas Bates <bates@stat.wisc.edu>
2227 :    
2228 :     * R/dtCMatrix.R: avoid coercion of dtCMatrix object to dgCMatrix
2229 :     in method for "t" so as not to lose the unit diagonal property.
2230 :    
2231 : bates 1257 2006-04-19 Douglas Bates <bates@stat.wisc.edu>
2232 :    
2233 :     * R/lmer.R, R/AllGeneric.R, NAMESPACE: Remove the postVar generic
2234 :     and methods. This is now an option to the ranef method for the
2235 :     mer class.
2236 :    
2237 :     * src/cs_utils.c: Ensure that the nz component is -1 for a
2238 :     compressed column-oriented matrix. Minor formatting cleanup.
2239 :    
2240 :     * man/lmer-class.Rd: Document the qqmath method for ranef.lmer
2241 :     objects.
2242 :    
2243 : maechler 1253 2006-04-19 Martin Maechler <maechler@stat.math.ethz.ch>
2244 :    
2245 :     * R/Auxiliaries.R (diagU2N): new for the solve() methods in
2246 :     * R/dtCMatrix.R: where dgC -> dgT coercion now preserves diag = "U".
2247 :    
2248 : bates 1251 2006-04-15 Douglas Bates <bates@stat.wisc.edu>
2249 :    
2250 :     * src/cs.[ch],src/cs_utils.[ch] : Added Tim Davis' CSparse library
2251 :     in cs.[ch] and utilities to interface to that code in cs_utils.[ch].
2252 :    
2253 :     * R/dtCMatrix.R, src/dtCMatrix.[ch] : CSparse-based solve methods
2254 :     for the dtCMatrix class.
2255 : maechler 1253
2256 : bates 1247 2006-04-12 Douglas Bates <bates@stat.wisc.edu>
2257 :    
2258 :     * R/pedigree.R, R/AllClass.R, NAMESPACE: added a pedigree class
2259 :     and methods for it.
2260 :    
2261 : maechler 1245 2006-04-12 Martin Maechler <maechler@stat.math.ethz.ch>
2262 :    
2263 :     * R/dgCMatrix.R: add storage.mode(.) <- "double" for "matrix"
2264 :     arguments, such that M %*% 1:6 now works
2265 :     * Tests/matprod.R: test the above
2266 :    
2267 : bates 1244 2006-04-03 Douglas Bates <bates@stat.wisc.edu>
2268 : bates 1243
2269 :     * R/lmer.R (qqmath,ranef.lmer-method): added a qqmath method for
2270 :     the ranef.lmer class.
2271 :    
2272 :     * R/AllClass.R, NAMESPACE, R/lmer.R: Added a postVar generic and
2273 :     methods to extract the posterior variances from the bVar slot.
2274 :    
2275 : maechler 1238 2006-03-30 Martin Maechler <maechler@stat.math.ethz.ch>
2276 :    
2277 :     * R/dtCMatrix.R: allow coercion from dgC* to triangular (dtC*)
2278 :     * R/dsCMatrix.R: and symmetric (dsC*) 'Csparse' matrices.
2279 :    
2280 :     * R/Tsparse.R: Tsparse* -> Csparse* coercion now works and is tested in
2281 :     * tests/simple: (extended)
2282 :    
2283 :     * R/sparseMatrix.R (isTriangular): now using much improved
2284 :     * R/Auxiliaries.R (isTriC): new triangularity check for *CMatrix
2285 :    
2286 : bates 1236 2006-03-23 Douglas Bates <bates@stat.wisc.edu>
2287 :    
2288 :     * src/dsyMatrix.c (dsyMatrix_as_dspMatrix): Propagate DimNames
2289 :     (problem report from Franklin Parlamis). This should be done
2290 : maechler 1238 generally.
2291 : bates 1236
2292 : bates 1234 2006-03-21 Douglas Bates <bates@stat.wisc.edu>
2293 :    
2294 :     * R/AllClass.R,lmer.R: Change the name of the lmer.ranef class to
2295 :     ranef.lmer (like summary.lmer). Add the coef.lmer class and
2296 :     update the plot methods.
2297 :    
2298 : bates 1232 2006-03-20 Douglas Bates <bates@stat.wisc.edu>
2299 :    
2300 :     * R/lmer.R (resid and ranef methods): Added methods for the
2301 :     "residuals" and "resid" generic but only for linear mixed model
2302 :     fits. Changed the ranef method to return a list of data frames so
2303 :     that the plot methods now work.
2304 :    
2305 : bates 1230 2006-03-16 Douglas Bates <bates@bates2>
2306 :    
2307 :     * src/dpoMatrix.c (dpoMatrix_chol): Require n > 0 in call to
2308 :     dpotrf - otherwise the BLAS on Mac OS X complains and quits.
2309 :    
2310 :     * DESCRIPTION (Date): New release
2311 :    
2312 : maechler 1228 2006-03-15 Martin Maechler <maechler@stat.math.ethz.ch>
2313 :    
2314 :     * DESCRIPTION (Version): 0.995-6 -- to be released to CRAN
2315 :    
2316 :     * data/KNex.rda: replacing 'mm' and 'y' by KNex <- list(mm=mm, y=y)
2317 :     * man/KNex.Rd: and other help files
2318 :     * tests/*.R: several ones needed adaption
2319 : bates 1352 * inst/doc/Comparisons.Rnw: ditto
2320 : maechler 1228
2321 : maechler 1226 2006-03-11 Martin Maechler <maechler@stat.math.ethz.ch>
2322 :    
2323 :     * R/dgCMatrix.R (replCmat): "[<-" methods for dgCMatrix
2324 :    
2325 :     * tests/indexing.R: tests for new [<- methods for sparse matrices.
2326 :    
2327 :     2006-03-10 Martin Maechler <maechler@stat.math.ethz.ch>
2328 :    
2329 :     * R/dgTMatrix.R (replTmat): "[<-" methods for dgTMatrix
2330 :    
2331 :     * R/Tsparse.R (.ind.prep): fix out-of-range indexing
2332 :    
2333 :     2006-03-08 Martin Maechler <maechler@stat.math.ethz.ch>
2334 :    
2335 :     * R/dMatrix.R: enable things like M [ M < 10 ]
2336 :     * R/dgeMatrix.R: implement it
2337 :    
2338 : maechler 1222 2006-03-06 Martin Maechler <maechler@stat.math.ethz.ch>
2339 :    
2340 :     * R/AllClass.R: define "summary.mer" and "*.lmer"
2341 :     * R/lmer.R (summary): summary(<mer>) computes & returns the above;
2342 :     * R/lmer.R (show): now works with summary()
2343 :    
2344 :     2006-03-04 Martin Maechler <maechler@stat.math.ethz.ch>
2345 :    
2346 :     * R/dgCMatrix.R: finally direct "Arith" dgC o dgC
2347 :     * R/Auxiliaries.R (WhichintersectInd): and other utilities to
2348 :     support the above
2349 :    
2350 : bates 1213 2006-02-07 Douglas Bates <bates@stat.wisc.edu>
2351 :    
2352 :     * R/lmer.R (lmer): fix initial values of offset and weights for glm.fit.
2353 :     Use glmFit$prior.weights for weights in a glmm.
2354 :     Allow an option usePQL = FALSE to skip the PQL steps for the
2355 :     Laplace method (and, in time, the AGQ method).
2356 :    
2357 :     * src/lmer.c (mer_factor): Move downdating and factoring of XtX
2358 :     into a separate function internal_mer_Xfactor to be able to call
2359 :     it from internal_bhat.
2360 :    
2361 : maechler 1200 2006-01-23 Martin Maechler <maechler@stat.math.ethz.ch>
2362 :    
2363 :     * tests/Class+Meth.R (tstMatrixClass): function for much better
2364 :     testing; now again of all actual classes.
2365 :    
2366 :     * src/Mutils.c (MAKE_TRIANGULAR_BODY, MAKE_SYMMETRIC_BODY):
2367 :     use macros and define make_d_matrix_* and make_i_matrix_*
2368 :     where _i_ is for the ldense routines:
2369 :    
2370 :     * src/ldense.c (ltrMatrix_as_lgeMatrix): provide functions
2371 :     * src/ldense.c (lsyMatrix_as_lgeMatrix):
2372 :    
2373 :     * R/ldenseMatrix.R: use the above in setAs(*,"lgeMatrix")
2374 :    
2375 :    
2376 : maechler 1174 2006-01-16 Martin Maechler <maechler@stat.math.ethz.ch>
2377 :    
2378 :     * R/Matrix.R (Matrix): has become much "smarter" now auto-producing
2379 :     many different kinds of matrices.
2380 :     * R/*.R: quite a few new methods were needed for R CMD check with
2381 :     new Matrix(). Very good for users playing around.
2382 :    
2383 :    
2384 : maechler 1165 2006-01-15 Martin Maechler <maechler@stat.math.ethz.ch>
2385 :    
2386 :     * src/dgeMatrix.c (dMatrix_validate): new
2387 :     * src/Mutils.c (dense_nonpacked_validate): new
2388 :    
2389 :     * src/dtrMatrix.c (dtrMatrix_validate): improved/fixed
2390 :    
2391 :    
2392 :     2006-01-14 Douglas Bates <bates@stat.wisc.edu>
2393 :    
2394 :     * R/AllClass.R (compMatrix), (generalMatrix): new virtual classes
2395 :    
2396 : bates 1123 2006-01-07 Douglas Bates <bates@stat.wisc.edu>
2397 : bates 1119
2398 : maechler 1127 * DESCRIPTION (Version): 0.99-6 released to CRAN
2399 :    
2400 : bates 1119 * src/dgBCMatrix.c (cscb_trcbsm): Fix due to Peter Dalgaard for
2401 :     segfault in cases with multiple non-nested grouping factors.
2402 :    
2403 : maechler 1109 2006-01-03 Martin Maechler <maechler@stat.math.ethz.ch>
2404 :    
2405 :     * DESCRIPTION (Version): 0.99-4 to be released to CRAN
2406 :     (Depends): also on 'utils'
2407 :    
2408 :     * R/AllClass.R (diagonalMatrix): new class with "ddi*" and "ldi*"
2409 :     * R/diagMatrix.R (Diagonal): constructor and methods for
2410 :     diagonal matrices
2411 :    
2412 :     * R/ltTMatrix.R: new "minimal methods"
2413 :    
2414 : maechler 1091 2005-12-12 Martin Maechler <maechler@stat.math.ethz.ch>
2415 :    
2416 :     * R/AllGeneric.R (tcrossprod): 2-argument version; here, and for
2417 :     all methods (and help files).
2418 :    
2419 : maechler 1084 2005-12-09 Martin Maechler <maechler@stat.math.ethz.ch>
2420 :    
2421 :     * R/Auxiliaries.R (dimNamesCheck): fixed thinko -> bug
2422 :     for case (dimn. op no_dimn.)
2423 :    
2424 :     2005-11-14 Douglas Bates <bates@stat.wisc.edu>
2425 :    
2426 : maechler 1174 * DESCRIPTION (Version): 0.99-2 released to CRAN
2427 : maechler 1084
2428 : bates 988 2005-10-21 Douglas Bates <bates@stat.wisc.edu>
2429 :    
2430 :     * R/lmer.R (simulate method): Fixed a drop=FALSE problem reported
2431 :     by Julian Faraway.
2432 :    
2433 : maechler 976 2005-10-06 Martin Maechler <maechler@stat.math.ethz.ch>
2434 :    
2435 :     * R/Auxiliaries.R (try_as): new utility
2436 :     * R/sparseMatrix.R: use try_as() in coercion to original class
2437 :    
2438 : maechler 956 2005-09-30 Martin Maechler <maechler@stat.math.ethz.ch>
2439 :    
2440 :     * src/dgCMatrix.c (double_to_csc): and dgeMatrix_to_csc()
2441 :    
2442 :     2005-09-29 Martin Maechler <maechler@stat.math.ethz.ch>
2443 :    
2444 :     * R/Auxiliaries.R (dimNamesCheck): added
2445 :    
2446 :     * R/Matrix.R (as.array), (as.vector): new
2447 :    
2448 : maechler 954 2005-09-28 Martin Maechler <maechler@stat.math.ethz.ch>
2449 :    
2450 :     * R/Matrix.R (Matrix): get logical argument 'sparse' with a smart
2451 : maechler 956 default.
2452 :     * R/AllClass.R: move 'factors' slot toplevel "Matrix";
2453 :     "pMatrix" now contains "sparseMatrix"
2454 : maechler 954
2455 : maechler 948 2005-09-26 Martin Maechler <maechler@stat.math.ethz.ch>
2456 :    
2457 :     * tests/Class+Meth.R: new tests; t(t(m)) == m
2458 :    
2459 :     * src/dtCMatrix.c (tsc_transpose): add forgotten "diag" slot
2460 :    
2461 :     * src/dsTMatrix.c (dsTMatrix_as_dsCMatrix): bad typo (segfault!)
2462 :     * src/dtTMatrix.c (dtTMatrix_as_dtCMatrix): new
2463 :    
2464 :     * R/dspMatrix.R: typo in "t" method
2465 :    
2466 : maechler 925 2005-09-18 Douglas Bates <bates@wisc.edu>
2467 :    
2468 :     * R/AllClass.R (TsparseMatrix), CsparseM* and RsparseM*
2469 :     * R/Tsparse.R: instead of R/gTMatrix.R
2470 :     * R/Csparse.R: new
2471 :     * src/Tsparse.c (Tsparse_to_Csparse): new; -> cholmod_()
2472 :     * src/Tsparse.c: new; many trivial methods calling cholmod_()
2473 :     * src/Csparse.c (Csparse_to_Tsparse), transpose, (mat|cross)prod:
2474 :     via cholmod
2475 :    
2476 :     2005-09-16 Martin Maechler <maechler@stat.math.ethz.ch>
2477 :    
2478 :     * R/Auxiliaries.R (non0ind): new function using new C code
2479 :     * src/dgCMatrix.c (compressed_non_0_ij): new utility
2480 :    
2481 : bates 917 2005-09-15 Douglas Bates <bates@localhost.localdomain>
2482 :    
2483 :     * src/chm_common.h: header file required by all C sources that
2484 : maechler 1174 call CHOLMOD functions. It defines a cholmod_common structure
2485 : bates 917 called 'c' whose address is passed as the last argument to
2486 :     (virtually) every CHOLMOD function.
2487 :    
2488 :     * src/Pattern.c: Simple example of the use of CHOLMOD.
2489 :    
2490 :     * src/init.c: initialize and finalize the cholmod_common structure.
2491 :    
2492 :     * src/Makefile: Added source packages CHOLMOD UMFPACK AMD COLAMD
2493 :     LDL and CCOLAMD from the U. of Florida sparse matrix library.
2494 :    
2495 : maechler 908 2005-09-08 Martin Maechler <maechler@stat.math.ethz.ch>
2496 :    
2497 :     * inst/test-tools.R: new file collecting the utility functions used
2498 :     in ./tests/*.R
2499 :    
2500 :     * R/ddenseMatrix.R (cbind2): new methods for "numeric" and "matrix"
2501 :     * R/Matrix.R (cbind2): methods for NULL and missing
2502 :    
2503 : maechler 886 2005-08-31 Martin Maechler <maechler@stat.math.ethz.ch>
2504 :    
2505 :     * R/AllClass.R: new "index" class for "[" and "[<-":
2506 :     First cut at "symmetricMatrix" and "triangularMatrix"
2507 :     * R/gTMatrix.R (.ind.prep): new function;
2508 : maechler 1174 Logical and character indexing now work too.
2509 : maechler 886 * R/Matrix.R: cheap "[<-" methods for denseMatrix now work
2510 :     * tests/indexing.R: new, including *.Rout.save
2511 :     * tests/dgTMatrix.R: new
2512 :    
2513 : bates 876 2005-08-29 Douglas Bates <bates@wisc.edu>
2514 :    
2515 :     * src/dgTMatrix.c (graphNEL_as_dgTMatrix): Corrected the position
2516 :     indicator pos not being updated. Also enforced upper triangular
2517 :     for symmetric case. Need to coerce edges component of elements of
2518 :     edge list - grr! (Why don't they define their classes cleanly?)
2519 :    
2520 : maechler 871 2005-08-26 Martin Maechler <maechler@stat.math.ethz.ch>
2521 :    
2522 :     * R/Matrix.R: added first "[<-" methods; not yet functional
2523 : bates 1352 * R/denseMatrix.R: ditto
2524 : maechler 871 * man/Subassign-methods.Rd: new help file for these
2525 :    
2526 :     2005-08-25 Martin Maechler <maechler@stat.math.ethz.ch>
2527 :    
2528 :     * DESCRIPTION (Version): 0.98-6
2529 :    
2530 :     * R/denseMatrix.R: new file for "[" fallback methods for all dense
2531 :     matrices.
2532 :    
2533 : maechler 868 2005-08-19 Martin Maechler <maechler@stat.math.ethz.ch>
2534 :    
2535 :     * src/lgCMatrix.c (lcsc_to_matrix): new; need for
2536 :     as( <logical>, "matrix")
2537 :    
2538 :     * R/pMatrix.R: coercion to "lgTMatrix"
2539 :    
2540 :     * R/gTMatrix.R: new virtual class to define "[" methods for.
2541 :     * man/gTMatrix-class.Rd:
2542 :     * General slight re-organization of where "[" methods are defined.
2543 :     more to come.
2544 :    
2545 : maechler 871 2005-08-18 Douglas Bates <bates@wisc.edu>
2546 : maechler 868
2547 : maechler 1174 * DESCRIPTION (Version): 0.98-5 released to CRAN
2548 : maechler 871
2549 :     * src/dgTMatrix.c (graphNEL_as_dgTMatrix): add first graphNEL methods
2550 :     * .....
2551 :    
2552 : bates 863 2005-08-18 Douglas Bates <bates@localhost.localdomain>
2553 :    
2554 :     * R/lmer.R: Corrected naming scheme in mcmcsamp to work with lmer
2555 :     or glmer objects.
2556 :    
2557 : maechler 860 2005-08-17 Martin Maechler <maechler@stat.math.ethz.ch>
2558 :    
2559 :     * DESCRIPTION (Version): 0.98-4 : upload to CRAN
2560 :    
2561 :     2005-08-16 Douglas Bates <bates@localhost.localdomain>
2562 :    
2563 :     * R/HBMM.R: finish re-writing R-only code.
2564 :    
2565 : bates 854 2005-08-15 Douglas Bates <bates@localhost.localdomain>
2566 :    
2567 :     * man/externalFormats.Rd: move documentation for writeHB and
2568 :     writeMM here.
2569 :    
2570 :     * src/mmio.c: replace inclusion of <malloc.h> by <stdlib.h>
2571 :     (suggested by Paul Roecker).
2572 :    
2573 :     * tests/validObj.R (assertError): Comment out test that is failing
2574 :     after recent changes in r-devel.
2575 :    
2576 : maechler 860
2577 : maechler 848 2005-08-11 Martin Maechler <maechler@stat.math.ethz.ch>
2578 :    
2579 :     * R/AllClass.R: intermediate virtual class "denseMatrix"
2580 :     * man/denseMatrix-class.Rd
2581 :     * NAMESPACE: export it, and also export
2582 :     * man/unused-classes.Rd: "iMatrix", "zMatrix" and "ldenseMatrix"
2583 :    
2584 : bates 846 2005-08-10 Douglas Bates <bates@wisc.edu>
2585 :    
2586 : maechler 848 * DESCRIPTION (Version): 0.98-3 to CRAN
2587 :    
2588 : bates 846 * src/dtrMatrix.c (dtrMatrix_validate): fixed up validation and
2589 :     matrix_solve code (which was really, really wrong).
2590 :    
2591 : bates 835 2005-08-07 Douglas Bates <bates@wisc.edu>
2592 : maechler 834
2593 :     * DESCRIPTION (Version): 0.98-2
2594 :    
2595 :     * R/HBMM.R (readHB), (readMM): read Matrix Market formats
2596 :    
2597 :     * R/lmer.R (abbrvNms): new
2598 :     * R/lmer.R (mcmcsamp): allow transformed parameters
2599 : bates 835 * src/HBMM.c (Matrix_writeMatrixMarket): Added read/write routines
2600 :     for the Harwell-Boeing and the MatrixMarket formats.
2601 : maechler 834
2602 :     2005-08-04 Martin Maechler <maechler@stat.math.ethz.ch>
2603 :    
2604 :     * man/dtrMatrix-class.Rd: add examples
2605 : bates 835 * man/dtpMatrix-class.Rd: ditto; plus note about PROBLEM
2606 : maechler 834
2607 :     * TODO: note the dtpMatrix (docu) bug
2608 :    
2609 :     * R/zzz.R (.onLoad): assignInNamespace("as.matrix", *, "base")
2610 :     in order to ensure that new as.matrix() is used by old functions,
2611 :     e.g., svd(), qr(), eigen(), dist(),..;
2612 :     apply(), also matplot() or pairs().
2613 :    
2614 :    
2615 :     2005-08-03 Martin Maechler <maechler@stat.math.ethz.ch>
2616 :    
2617 :     * R/lmer.R: add 'fixme' comments and move the linear vs glm check;
2618 :     add comments about 'control' / lmerControl() arguments
2619 :    
2620 : bates 835 2005-07-27 Douglas Bates <bates@wisc.edu>
2621 : bates 820
2622 : bates 835 * man/sleepstudy.Rd: Added the sleep data set.
2623 : maechler 1174 * DESCRIPTION (Version): 0.98-1 released to CRAN
2624 : bates 820
2625 : bates 835 2005-07-12 Douglas Bates <bates@wisc.edu>
2626 : maechler 834 * man/sleepstudy.Rd: Added the sleep data set.
2627 :    
2628 : bates 809 * R/lmer.R (glmmMCMC): Added PACKAGE = "Matrix" in a couple of
2629 :     .Call calls that were producing spurious output.
2630 :    
2631 : bates 835 2005-07-05 Douglas Bates <bates@wisc.edu>
2632 : bates 801
2633 :     * R/lmer.R (lmer): stored updated variance component estimates in
2634 :     mer object for the generalized model. (Bug reported by Renaud
2635 :     Lancelot).
2636 :    
2637 : bates 835 2005-07-03 Douglas Bates <bates@wisc.edu>
2638 : bates 794
2639 :     * src/lmer.c (glmer_devAGQ): Added AGQ for single grouping factor,
2640 :     unidimensional case.
2641 :    
2642 : bates 835 2005-06-08 Douglas Bates <bates@wisc.edu>
2643 : maechler 791
2644 :     * DESCRIPTION (Version): 0.96-1
2645 :    
2646 : maechler 1174 * moved lmer-class' R and C code moved from lme4 to here
2647 : maechler 791
2648 : bates 835 2005-06-04 Douglas Bates <bates@wisc.edu>
2649 : bates 763
2650 :     * R/dgCMatrix.R: Call to csc_matrix_mm used undefined arguments
2651 :     (reported by Guissepe Ragusa <gragusa@ucsd.edu>)
2652 :    
2653 : bates 835 2005-06-02 Douglas Bates <bates@wisc.edu>
2654 : bates 763
2655 :     * src/Makefile.win: Forgot to update this when Makefile changed.
2656 :    
2657 : bates 835 2005-05-11 Douglas Bates <bates@wisc.edu>
2658 : bates 726
2659 :     * src/dgCMatrix.c (csc_transpose): Simplified function fixing a
2660 :     bug reported by Kurt Hornik and Michael Hahsler.
2661 :    
2662 : bates 835 2005-05-10 Douglas Bates <bates@wisc.edu>
2663 : bates 725
2664 :     * src/lgCMatrix.c (Matrix_lgClgCmm): Implementation of methods for
2665 :     logical sparse matrices. These will also be used in the symbolic
2666 :     analysis for lmer objects.
2667 :    
2668 :     * src/dsCMatrix.c (dsCMatrix_matrix_solve): Copied the dimensions
2669 :     of b to the result. Fixes bug reported by Jean.Coursol@math.u-psud.fr
2670 : maechler 791
2671 : bates 835 2005-05-06 Douglas Bates <bates@wisc.edu>
2672 : bates 714
2673 :     * src/dgeMatrix.c (dgeMatrix_colsums): Added an implementation of
2674 :     colMeans, colSums, rowMeans and rowSums.
2675 :    
2676 : bates 835 2005-04-18 Douglas Bates <bates@wisc.edu>
2677 : bates 692
2678 :     * src/lgCMatrix.[ch]: code for _validate method and stub for
2679 :     multiplication operation.
2680 :    
2681 :     * src/dgeMatrix.c (dgeMatrix_matrix_solve): Passing wrong argument
2682 :     to dgetrs.
2683 :    
2684 :     * src/init.c: Fix cut-and-paste error in definition of
2685 :     dgeMatrix_matrix_solve
2686 :    
2687 :     * src/{many files}: Tighten code by using ALLOC_SLOT.
2688 :    
2689 : bates 835 2005-04-15 Douglas Bates <bates@wisc.edu>
2690 : bates 692
2691 :     * R/AllClass.R: Add lgTMatrix and lgCMatrix classes
2692 :    
2693 :     * DESCRIPTION: Eliminate import of stats.
2694 :    
2695 : maechler 791
2696 : bates 835 2005-04-06 Douglas Bates <bates@wisc.edu>
2697 : bates 692
2698 :     * R/AllClass.R : add logical sparse matrix classes
2699 :    
2700 : maechler 687 2005-04-01 Martin Maechler <maechler@stat.math.ethz.ch>
2701 :    
2702 :     * R/dgTMatrix.R: add "[" method for triplet matrices
2703 :     * R/sparseMatrix.R: and other sparse ones; --> add show() for sparse
2704 :    
2705 : bates 835 2005-03-31 Douglas Bates <bates@wisc.edu>
2706 : maechler 687
2707 :     * DESCRIPTION (Version): release 0.95-5 to CRAN
2708 :    
2709 :     * R/dMatrix.R: add %*%, crossprod and solve "fallback" methods
2710 :     * R/sparseMatrix.R: %*%, crossprod()
2711 :     * R/dgeMatrix.R: more "fallback" methods for numeric/dense matrices
2712 :     * man/*.Rd: move method definitions to 'Matrix' and 'dMatrix'
2713 :     * src/lmer.c (lmer_fitted): fix thinko
2714 :    
2715 : maechler 676 2005-03-26 Martin Maechler <maechler@stat.math.ethz.ch>
2716 :    
2717 :     * R/AllClass.R: add two virtual sparse classes ``on top''
2718 :    
2719 :     2005-03-24 Martin Maechler <maechler@stat.math.ethz.ch>
2720 :    
2721 :     * R/AllClass.R (setClass): use "VIRTUAL" for the virtual classes;
2722 :     correspondingly fix examples and tests/ since new()
2723 :     doesn't work for virtual classes.
2724 :    
2725 : maechler 658 2005-03-17 Martin Maechler <maechler@stat.math.ethz.ch>
2726 :    
2727 :     * R/Matrix.R (as.matrix): method and one for unname()
2728 :     * tests/dpoMatrix.R: tests should now be less platform dependent;
2729 :     also run for R 2.1.0; using as.matrix()
2730 :    
2731 : bates 835 2005-03-15 Douglas Bates <bates@wisc.edu>
2732 : maechler 658
2733 :     * R/pMatrix.R: "pMatrix" class added
2734 :     * ....
2735 :    
2736 : bates 835 2005-03-14 Douglas Bates <bates@wisc.edu>
2737 : bates 645
2738 :     * R/dtpMatrix.R: Add unpack method and an example.
2739 :    
2740 :     * src/dsyMatrix.c (dsyMatrix_trf): Add BunchKaufman factorization
2741 :     of general symmetric matrices and associated S4 methods.
2742 :    
2743 : maechler 658 2005-03-10 Martin Maechler <maechler@stat.math.ethz.ch>
2744 :     +
2745 :     2005-03-05 Martin Maechler <maechler@stat.math.ethz.ch>
2746 :    
2747 :     * R/dgeMatrix.R (setAs): and many other files: more coercion,
2748 :     crossprod() and "%*%" methods added; tests, too.
2749 :     * tests/matprod.R: new, for testing these
2750 :    
2751 : bates 835 2005-03-03 Douglas Bates <bates@wisc.edu>
2752 : bates 599
2753 :     * src/lmer.c (lmer_fitted): Added.
2754 :    
2755 : bates 835 2005-03-02 Douglas Bates <bates@wisc.edu>
2756 : bates 596
2757 :     * R/dsTMatrix.R: Conversion from dsTMatrix to dsCMatrix
2758 :    
2759 : bates 835 2005-02-28 Douglas Bates <bates@wisc.edu>
2760 : bates 582
2761 :     * src/*.c,po/,inst/po: Internationalization and localization of
2762 :     the package.
2763 :    
2764 :     * src/ldl.[ch]: Removed these as their contents are referenced in the
2765 :     R_ldl.c file.
2766 :    
2767 :     * src/flame.[ch]: Removed these source files.
2768 : maechler 658
2769 : bates 582 * src/dtrMatrix.c (make_array_triangular): Move to Mutils
2770 :    
2771 :     * src/LU.[ch],src/init.c: absorb in factorizations
2772 :    
2773 :     * src/Mutils.h: prepare for internationalization
2774 :    
2775 :     * src/cblas.h: move the enum definitions to Mutils.h and remove
2776 :     this file
2777 :    
2778 : maechler 578 2005-02-26 Martin Maechler <maechler@stat.math.ethz.ch>
2779 :    
2780 : maechler 579 * R/dgeMatrix.R: provide "dimnames" and "dimnames<-" methods
2781 :    
2782 :     * R/dtrMatrix.R: fix t() method
2783 :    
2784 : maechler 578 * R/dgeMatrix.R: define group methods "Arith", "Math", "Math2"
2785 : maechler 658 * NAMESPACE: export them (and import generics from "methods")
2786 : maechler 578 * tests/group-methods.R : and test them.
2787 :    
2788 :     * src/dtrMatrix.c (dtrMatrix_as_dgeMatrix): prevent seg.fault in
2789 :     border case
2790 :    
2791 :     2005-02-24 Douglas Bates <bates@stat.wisc.edu>
2792 :    
2793 : maechler 658 * DESCRIPTION (Version): 0.95-2 released to CRAN
2794 : maechler 578
2795 :     * src/dgBCMatrix.c:
2796 :     * src/lmer.c: many changes
2797 :     * ...
2798 :    
2799 : maechler 512 2005-02-04 Martin Maechler <maechler@stat.math.ethz.ch>
2800 :    
2801 :     * R/Matrix.R: add more sophisticated show() method.
2802 :    
2803 : maechler 578 2005-02-02 Douglas Bates <bates@stat.wisc.edu>
2804 :    
2805 :     * */* : almost complete reorganization of classes.
2806 :    
2807 : bates 835 2005-01-26 Douglas Bates <bates@wisc.edu>
2808 : bates 460
2809 :     * R/AllGeneric.R: Added matrix exponential generic expm and a method
2810 :     for the geMatrix class.
2811 :    
2812 : bates 835 2005-01-24 Douglas Bates <bates@wisc.edu>
2813 : bates 460
2814 :     * src/Makefile (clean): Remove *.a and *.so
2815 :    
2816 :     * man/cscBlocked-class.Rd: Remove reference to the lmer-class.
2817 :    
2818 : bates 835 2005-01-23 Douglas Bates <bates@wisc.edu>
2819 : bates 460
2820 : maechler 658 * src/lmer.c (Lind): Definition of Lind was backwards. This only
2821 : bates 460 had an effect in cases with more than 2 grouping factors.
2822 :    
2823 : bates 835 2005-01-03 Douglas Bates <bates@wisc.edu>
2824 : bates 415
2825 :     * src/lmeRep.c (lmer_variances): change from lmeRep to lmer
2826 :    
2827 : bates 835 2004-12-23 Douglas Bates <bates@wisc.edu>
2828 : bates 410
2829 :     * src/init.c (R_init_Matrix): Reorder calls to R_registerRoutines
2830 :     and R_useDynamicSymbols (suggested by B.D.Ripley).
2831 :    
2832 : bates 835 2004-12-14 Douglas Bates <bates@wisc.edu>
2833 : bates 392
2834 :     * R/sscMatrix.R: Add determinant methods
2835 :    
2836 :     * src/triplet.[ch],src/init.c (triplet_to_matrix): Add a coercion
2837 :     for tripletMatrix to matrix.
2838 :    
2839 : bates 835 2004-12-13 Douglas Bates <bates@wisc.edu>
2840 : bates 388
2841 : bates 392 * R/AllClass.R (.onLoad): Eliminate the bbCrosstab class, which is
2842 :     no longer used.
2843 :    
2844 : bates 388 * src/R_ldl.c: Created an R-specific version of the ldl.[ch] files
2845 :     with dynamic allocation of scratch arrays.
2846 :    
2847 :     * src/ssclme.c (ssclme_copy_ctab): Fixed bug in creation of ZtZ
2848 :     for multivariate random effects with multiple grouping factors.
2849 :     Fixes part but not all of #15.
2850 :    
2851 : bates 835 2004-12-03 Douglas Bates <bates@wisc.edu>
2852 : bates 375
2853 :     * src/lmeRep.c (lmeRep_factor): order of operations for multiple
2854 :     scalar grouping factors corrected.
2855 :    
2856 : bates 835 2004-11-29 Douglas Bates <bates@wisc.edu>
2857 : bates 375
2858 :     * src/bCrosstab.c: remove diag_update which is no longer used
2859 :    
2860 : bates 835 2004-11-16 Douglas Bates <bates@wisc.edu>
2861 : bates 350
2862 :     * src/Metis_utils.c: Move metis.h include to C sources so that the
2863 :     .h file can be included.
2864 :    
2865 : bates 835 2004-11-12 Douglas Bates <bates@wisc.edu>
2866 : bates 342
2867 : bates 350 * src/LU.c,geMatrix.c,trMatrix.c, etc.:
2868 : bates 342 Complete allocation of slots in NEW_OBJECT.
2869 :    
2870 :     * src/Mutils.h: Moved list of symbols to an include file
2871 :    
2872 : bates 835 2004-11-11 Douglas Bates <bates@wisc.edu>
2873 : bates 342
2874 :     * src/geMutils.c (Matrix_init): remove unused function
2875 :    
2876 : bates 835 2004-11-10 Douglas Bates <bates@wisc.edu>
2877 : bates 342
2878 :     * src/cscMatrix.c (csc_to_imagemat): removed unused function
2879 :    
2880 : bates 835 2004-11-05 Douglas Bates <bates@wisc.edu>
2881 : bates 327
2882 :     * src/Makefile.win (SOURCES_C): Keep consistent with Makefile
2883 :    
2884 : bates 835 2004-10-27 Douglas Bates <bates@wisc.edu>
2885 : bates 303
2886 :     * R/pdmatrix.R: remove PACKAGE="Matrix" in .Call calls
2887 :    
2888 : bates 835 2004-10-04 Douglas Bates <bates@wisc.edu>
2889 : bates 296
2890 :     * src/init.c: Created R_init_Matrix and added registration of C
2891 :     routines.
2892 :    
2893 : bates 835 2004-10-02 Douglas Bates <bates@wisc.edu>
2894 : bates 283
2895 :     * R/tripletMatrix.R: Force a require(lattice) for the image methods.
2896 :    
2897 : bates 835 2004-06-15 Douglas Bates <bates@wisc.edu>
2898 : bates 229
2899 :     * man/trMatrix-class.Rd: Escape the % chars in .Rd files.
2900 :    
2901 : bates 111 2004-04-20 Douglas Bates <bates@stat.wisc.edu>
2902 :    
2903 :     * src/Makefile.win ($(SHLIB)): Modifications per Uwe Ligges.
2904 :    
2905 : bates 109 2004-04-19 Douglas Bates <bates@stat.wisc.edu>
2906 :    
2907 :     * src/ssclme.c (ssclme_update_mm): fix logic error in
2908 :     ssclme_update_mm
2909 :    
2910 : bates 105 2004-04-18 Douglas Bates <bates@stat.wisc.edu>
2911 :    
2912 :     * src/ssclme.c (ssclme_coef, ssclme_coefGets): Create consistency
2913 :     in the order of unconstrained and constrained parameters.
2914 :     (ssclme_gradient): Added the gradients (not yet correct for
2915 :     multidimensional, unconstrained case).
2916 :    
2917 : bates 78 2004-04-14 Douglas Bates <bates@stat.wisc.edu>
2918 :    
2919 :     * src/ssclme.c (ssclme_EMsteps): Fix logic in REML update
2920 :    
2921 :     * src/Makefile.win: Remove unneeded ranlib call
2922 :    
2923 : bates 71 2004-04-12 Douglas Bates <bates@stat.wisc.edu>
2924 :    
2925 :     * DESCRIPTION (Version): New release
2926 :    
2927 :     * src/Makefile.win: Update Makefile.win to umfpack removal.
2928 :    
2929 : bates 49 2004-04-05 Douglas Bates <bates@bates2_home>
2930 :    
2931 :     * src/triplet_to_col.c: Create triplet_to_col as a native
2932 : maechler 658 function, not the version from umfpack. There were problems with
2933 : bates 49 the configuration of UMFPACK for 64-bit processors and there was
2934 :     only one umfpack routine being used so I moved it here.
2935 :    
2936 : bates 45 2004-04-04 Douglas Bates <bates@bates2_home>
2937 :    
2938 :     * src/ssclme.c (ssclme_variances): New function.
2939 :    
2940 : bates 28 2004-03-28 Douglas Bates <bates@bates2_home>
2941 :    
2942 :     * src/ssclme.c (ssclme_fitted): Added function.
2943 :    
2944 : bates 22 2004-03-27 Douglas Bates <bates@bates2_home>
2945 :    
2946 :     * src/ssclme.c (ssclme_transfer_dimnames): Add new function to
2947 :     store the dimnames in the XtX and bVar slots
2948 :     (ssclme_update_mm): Change the dimensions of the bVar slot
2949 :     components and the returned value from ssclme_ranef.
2950 :    
2951 : bates 10 2004-03-18 Douglas Bates <bates@stat.wisc.edu>
2952 :    
2953 :     * R/{pdMat.R,pdIdent.R,pdLogChol.R,pdMatrixLog.R,pdNatural.R},
2954 :     src/{pdMat.c,pdIdent.c,pdLogChol.c,pdNatural.c},
2955 :     tests/{pdCompSymm.R,pdDiag.R,pdIdent.R,pdLogChol.R,pdNatural.R},
2956 :     man/{pdMat-class.Rd,pdmatrix-class.Rd,corrmatrix-class.Rd,
2957 :     pdDiag-class.Rd,pdIdent-class.Rd,pdNatural-class.Rd,
2958 :     pdLogChol-class.Rd,coefGets.Rd,pdCompSymm-class.Rd,
2959 :     pdfactor-class.Rd,pdFactor.Rd,pdMatrix.Rd,
2960 :     pdBlocked-class.Rd},AllClass.R,AllGeneric.R:
2961 :     Moved the pdMat classes from the lme4 package.
2962 :    
2963 :     2004-03-02 Douglas Bates <bates@stat.wisc.edu>
2964 :    
2965 :     * man/ssclme-class.Rd: Update definition and documentation of the
2966 :     ssclme class to include the DIsqrt slot.
2967 :    
2968 :     * src/ssclme.c (ssclme_deviance): Modify order of computation
2969 :     (much faster using dsyrk, a level 3 BLAS routine).
2970 :    
2971 :     * src/Makefile (SUBLIBS): Change definition (K. Hornik)
2972 :    
2973 :     2004-02-28 Douglas Bates <bates@stat.wisc.edu>
2974 :    
2975 :     * tests/ssclme.R: Modify the test to account for the permutation
2976 :     of the levels of the grouping factors.
2977 :    
2978 :     2004-02-23 Douglas Bates <bates@stat.wisc.edu>
2979 :    
2980 :     * R/ssclme.R,src/ssclme.c (ssclme): Move slots of sscCrosstab slot
2981 :     directly into the ssclme class definition.
2982 :    
2983 :     2004-02-22 Douglas Bates <bates@stat.wisc.edu>
2984 :    
2985 :     * DESCRIPTION (Date): New release
2986 :    
2987 :     * man/ssclme-class.Rd: new file.
2988 :    
2989 :     * src/ssclme.c (ssclme_loglik): major revisions in design. It
2990 :     works and it's fast!
2991 :    
2992 :     2004-02-17 Douglas Bates <bates@stat.wisc.edu>
2993 :    
2994 :     * src/taucs/Makefile.win (lib): Change "ar" to "$(AR)" (B.Ripley)
2995 :    
2996 :     2004-02-16 Douglas Bates <bates@stat.wisc.edu>
2997 :    
2998 :     * DESCRIPTION (Date): New release
2999 :    
3000 :     * NAMESPACE: Don't export ssclme.
3001 :    
3002 :     * data/ScotsSec.rda, man/ScotsSec.Rd: Add Scottish secondary
3003 :     school data.
3004 :    
3005 :     2004-02-11 Douglas Bates <bates@stat.wisc.edu>
3006 :    
3007 :     * src/sscCrosstab.c (sscCrosstab): Added a row to the incidence to
3008 :     keep track of the fixed-effects and the response. Counts also
3009 :     gets an extra element, which is always one.
3010 :    
3011 :     * src/ldl.c: Include these routines from Tim Davis' LDL package.
3012 :    
3013 :     2004-02-10 Douglas Bates <bates@stat.wisc.edu>
3014 :    
3015 :     * src/cscMatrix.c (csc_transpose): new function
3016 :    
3017 :     * src/Mutils.c (csc_sort_columns): perm/iperm confusion corrected
3018 :     (csc_components_transpose): new function
3019 :    
3020 :     2004-02-06 Douglas Bates <bates@stat.wisc.edu>
3021 :    
3022 :     * src/triplet.c (triplet_validate): Fix Dim slot on generated
3023 :     triplets
3024 :    
3025 :     2004-01-30 Douglas Bates <bates@stat.wisc.edu>
3026 :    
3027 :     * R/sscCrosstab.R (sscCrosstab): Added sscCrosstab generator function.
3028 :    
3029 :     * src/LU.h (MATRIX_LU_H): Add #ifndef #define ... #endif to this
3030 :     and all other .h files in src.
3031 :    
3032 :     * src/Makefile.win: This and other Makefile.win files contributed
3033 :     by Brian Ripley.
3034 :    
3035 :     2004-01-27 Douglas Bates <bates@stat.wisc.edu>
3036 :    
3037 :     * R/syMatrix.R: Added methods for "%*%".
3038 :    
3039 :     * R/Hilbert.R (Hilbert): Changed Hilbert function to return a
3040 :     poMatrix object.
3041 :    
3042 :     2004-01-26 Douglas Bates <bates@stat.wisc.edu>
3043 :    
3044 :     * man/sscChol-class.Rd,man/mm.Rd,man/y.Rd: Added man pages.
3045 :    
3046 :     2004-01-25 Douglas Bates <bates@bates2_home>
3047 :    
3048 :     * inst/doc/Introduction.Rnw,Comparisons.Rnw: Added vignettes.
3049 :    
3050 :     * R/csc.R: Convert all cscMatrix classes to use Dim slot instead
3051 :     of nrow.
3052 :    
3053 :     2003-12-31 Douglas Bates <bates@stat.wisc.edu>
3054 :    
3055 :     * src/taucs/taucs.h: Moved taucs.h, amd.h, and umfpack.h into
3056 :     subdirectories.
3057 :    
3058 :     2003-12-08 Douglas Bates <bates@stat.wisc.edu>
3059 :    
3060 :     * src/taucs.h: Accidently referred to global header files
3061 :     instead of local files.
3062 :    
3063 :     2003-12-04 Douglas Bates <bates@stat.wisc.edu>
3064 :    
3065 :     * R/AllClass.R: Lots of changes. Removed all the lapack++ code
3066 :     and methods and replaced all classes with S4 classes.
3067 :    
3068 :     2003-04-19 Douglas Bates <bates@stat.wisc.edu>
3069 :    
3070 :     * R/det.R,man/det.Rd: Change name of det generic to determinant
3071 :    
3072 :     * src/R_LapackPP.cc: Change method of calculating determinants
3073 :    
3074 :     2003-02-03 Douglas Bates <bates@stat.wisc.edu>
3075 :    
3076 :     * DESCRIPTION (Version): removed empty data directory as requested
3077 :     by CRAN maintainers. Changed version number and date.
3078 :    
3079 :     2002-10-23 Douglas Bates <bates@stat.wisc.edu>
3080 :    
3081 :     * src/laindex.h: Applied patches from Brian Ripley for compilation
3082 :     under Windows.
3083 :    
3084 :     * Added configure.win and src/Makevars.win as requested by Brian
3085 :     Ripley.
3086 :    
3087 :     2002-05-03 Douglas Bates <bates@stat.wisc.edu>
3088 :    
3089 :     * src/lamatrix.h: Removing pre-1.2.0 compatibility code per Kurt
3090 :     Hornik.
3091 :    
3092 :     2002-04-24 Douglas Bates <bates@stat.wisc.edu>
3093 :    
3094 :     * configure.ac: Replaced configure.in with configure.ac
3095 :     contributed by Kurt Hornik.
3096 :    
3097 :     * aclocal.m4 (ac_clean_files): Replaced this with Kurt Hornik's
3098 :     version for R-1.5.0
3099 :    
3100 : maechler 512
3101 : bates 10 2001-12-10 Douglas Bates <bates@stat.wisc.edu>
3102 :    
3103 :     * man/eigen.Rd: Removed the .Alias in the example

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