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Annotation of /pkg/ChangeLog

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

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