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Annotation of /pkg/ChangeLog

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1 : mmaechler 2207 2008-07-07 Martin Maechler <maechler@stat.math.ethz.ch>
2 :    
3 :     * R/sparseVector.R (spV2M): fix for "isparseVector".
4 :     Further, fix <diag> -> <sparseVector> coercion
5 :     (repSpV): add rep(<sparseVector>, .) method
6 :    
7 :     * R/sparseMatrix.R ([<-): when the RHS is a "scarce"Matrix, do *not*
8 :     use as.vector(.).
9 :    
10 :     * R/[TCR]sparse.R ([<-): methods for value = "sparseVector"
11 :    
12 :     * R/AllClass.R: new (hidden) class union "scarceMatrix"
13 :     * R/AllClass.R: sparseVector: add prototype
14 :    
15 :     * src/dsCMatrix.c (chk_nm): fix "Cholesky" check, thanks to Kasper Kristensen
16 :    
17 :     2008-06-28 Martin Maechler <maechler@stat.math.ethz.ch>
18 :    
19 :     * tests/other-pkgs.R: add more interesting Matrix -> graph
20 :    
21 :     2008-06-27 Martin Maechler <maechler@stat.math.ethz.ch>
22 :    
23 :     * R/sparseMatrix.R (Tsp2grNEL): add 'need.uniq' argument for speed
24 :     improvement in "[CR]sparseMatrix" -> "graphNEL" coercion.
25 :    
26 : mmaechler 2206 2008-06-25 Martin Maechler <maechler@stat.math.ethz.ch>
27 :    
28 :     * R/diagMatrix.R (.bdiag): use more efficient Bates-algorithm for
29 :     .bdiag().
30 :     * man/bdiag.Rd: update, including test.
31 :    
32 :     2008-06-24 Martin Maechler <maechler@stat.math.ethz.ch>
33 :    
34 :     * tests/Simple.R: add minimal bdiag() checks
35 :    
36 :     * R/diagMatrix.R (bdiag): fix bdiag(diag(4:5)) case;
37 :     factor out the Tsparse - internal computation into new .bdiag()
38 :    
39 : mmaechler 2203 2008-06-14 Martin Maechler <maechler@stat.math.ethz.ch>
40 :    
41 :     * R/nsparseMatrix.R: specific fast all() and any() methods.
42 :    
43 :     * src/dgTMatrix.c (MAKE_gTMatrix_to_geMatrix): better error message
44 :     when trying to produce too large result.
45 :    
46 :     * inst/test-tools.R (checkMatrix): add 'do.matrix' with a check for
47 :     very large matrices.
48 :    
49 :     * R/sparseMatrix.R (printSpMatrix2): new function, used by
50 :     show(<sparseMatrix>).
51 :    
52 :     * R/diagMatrix.R (show): print only diagonal entries when nrow(.) >= 50.
53 :    
54 :     2008-06-13 Martin Maechler <maechler@stat.math.ethz.ch>
55 :    
56 :     * src/Mutils.c (m_encodeInd, m_encodeInd2):
57 :     * R/*.R: .Call(m_encodeInd2?, ..) instead of encodeInd2?(..).
58 :    
59 :     * R/Auxiliaries.R (encodeInd2?): care against integer overflow (for
60 :     big matrices): -> 2nd argument 'di' instead of 'nr' !
61 :    
62 : mmaechler 2202 2008-06-09 Martin Maechler <maechler@stat.math.ethz.ch>
63 :    
64 :     * R/dtCMatrix.R: faster dgC* -> dtC* method
65 :     * tests/Simple.R: (hence removed "FIXME")
66 :    
67 :     * R/Auxiliaries.R (copyClass): add 'check = .copyClass.check'
68 :     which can be be turned off for possible speed gains.
69 :    
70 : mmaechler 2199 2008-06-02 Martin Maechler <maechler@stat.math.ethz.ch>
71 :    
72 :     * R/dMatrix.R, R/Tsparse.R: get rid of some disambiguation warnings
73 :    
74 :     * R/not.R: fix !<ldiMatrix>
75 :     implement two old "FIXME"s: !<ldenseMatrix> & !<ndenseMatrix>
76 :    
77 :     * R/diagMatrix.R (Ops): fix one-off thinko in
78 :     <diagonal> o <numeric> methods
79 :    
80 :     * inst/test-tools.R: checkMatrix(): drop0(m12) unconditionally
81 :    
82 : mmaechler 2196 2008-05-30 Martin Maechler <maechler@stat.math.ethz.ch>
83 :    
84 :     * R/diagMatrix.R (Ops): more <diagonal> o <Matrix> methods
85 :     * tests/Simple.R: testing the above
86 :    
87 : mmaechler 2194 2008-05-07 Martin Maechler <maechler@stat.math.ethz.ch>
88 :    
89 :     * NAMESPACE: also import "Ops" {found via new tools:::get_S4_generics_with_methods()}
90 :    
91 : mmaechler 2193 2008-05-03 Martin Maechler <maechler@stat.math.ethz.ch>
92 :    
93 :     * R/Matrix.R (dimnames<-): dimnames(.) <- NULL works with a message;
94 :     * NAMESPACE (unname): finally exported
95 :    
96 : mmaechler 2186 2008-04-28 Martin Maechler <maechler@stat.math.ethz.ch>
97 :    
98 : mmaechler 2190 * R/Auxiliaries.R (cholMat): possibly keep packed
99 :    
100 : mmaechler 2188 * inst/test-tools.R (checkMatrix): add fixed determinant.matrix()
101 :     for R < 2.7.0.
102 :    
103 : mmaechler 2186 * R/Tsparse.R ([): for triangularMatrix, check if result may be
104 :     triangular.
105 :     * tests/indexing.R: regression test
106 :    
107 : mmaechler 2185 2008-04-26 Martin Maechler <maechler@stat.math.ethz.ch>
108 :    
109 :     * inst/test-tools.R (checkMatrix): test <Ops> not only for dMatrix
110 :     * R/Ops.R: more methods, for lMatrix/nMatrix
111 :    
112 : mmaechler 2183 2008-04-24 Martin Maechler <maechler@stat.math.ethz.ch>
113 :    
114 :     * R/expm.R: new file for all expm() methods; notably new ones for
115 :     diagonal*, triangular*, symmetric* and also simple "matrix".
116 :    
117 : mmaechler 2175 2008-04-23 Martin Maechler <maechler@stat.math.ethz.ch>
118 :    
119 : mmaechler 2183 * R/dsyMatrix.R: setAs(.) rather than setIs(.) "to dpoMatrix"
120 :    
121 :     * inst/test-tools.R (assert.EQ.mat): better message when not equal
122 :    
123 :     * src/dgeMatrix.c (dgeMatrix_matrix_crossprod): allow integer RHS.
124 :    
125 :     * R/AllClass.R (ddiMatrix,ldiMatrix): extend [dl]Matrix instead of
126 :     [dl]denseMatrix {identical slots; but more logical method dispatch}
127 :    
128 :     2008-04-23 Martin Maechler <maechler@stat.math.ethz.ch>
129 :    
130 : mmaechler 2175 * R/sparseMatrix.R (summary): use length(<i-slot>) instead of nnzero()
131 :    
132 :     * R/diagMatrix.R (determinant): method
133 :    
134 :     2008-04-22 Martin Maechler <maechler@stat.math.ethz.ch>
135 :    
136 :     * src/dsCMatrix.c (dsCMatrix_Cholesky): suppress CHOLMOD printing too
137 :    
138 :     * R/Rsparse.R (.viaC.to.R): uplo fix for symmetric & triangular
139 :    
140 :     * R/dsCMatrix.R (determinant): switch to use Cholesky( 'LDL' ) and
141 :     its diagonal
142 :    
143 :     2008-04-21 Martin Maechler <maechler@stat.math.ethz.ch>
144 :    
145 :     * R/dMatrix.R (Summary): short-cut for prod(<sparse>)
146 :    
147 :     * R/not.R: fix !<"U"-diag-ltrMatrix> ; drop {R < 2.6.0}-branch
148 :    
149 :     * R/Auxiliaries.R (tT2gT): fix for "U"-diag-ltTMatrix
150 :    
151 :     * R/AllClass.R: ltTMatrix validity: call (more stringent) tTMatrix_validate
152 :    
153 :     2008-04-19 Martin Maechler <maechler@stat.math.ethz.ch>
154 :    
155 :     * R/Ops.R (Ops.x.x): aux.function, not just for (dMatrix,dMatrix)
156 :    
157 :     * R/Ops.R (.do.Logic.lsparse): fix NA case
158 :    
159 :     * R/Tsparse.R (replTmat): fix r.sym case, using indTri()
160 :    
161 :     * R/Auxiliaries.R (nnzero): fix special cases, using
162 :     * R/Auxiliaries.R (indDiag): new utility
163 :     * R/Auxiliaries.R (indTri): new argument 'diag'
164 :    
165 :     * R/dMatrix.R: Summmary(<ddenseMatrix>): different branch for dsy*
166 :    
167 :     2008-04-18 Martin Maechler <maechler@stat.math.ethz.ch>
168 :    
169 :     * R/diagMatrix.R: "Summary" methods, and more "Arith" / "Ops"
170 :    
171 :     * src/Csparse.c (Csparse_drop): preserve (uplo,diag) for
172 :     ".tCMatrix" triangular matrix.
173 :    
174 :     * R/Auxiliaries.R (drop0): use diagU2N(); according to helpfile,
175 :     'clx' can be class *or* class representation.
176 :     (nnzSparse): new.
177 :     (non0ind): new 'xtendSymm' argument; used in
178 :     * R/Ops.R:
179 :    
180 :     * R/pMatrix.R: more efficient determinant() method
181 :    
182 :     2008-04-17 Martin Maechler <maechler@stat.math.ethz.ch>
183 :    
184 :     * [disactivated] R/Matrix.R (det): det() as base::det(), but with Matrix environment
185 :     * [disactivated] NAMESPACE: export(det)
186 :    
187 :     * R/diagMatrix.R (mkDiag): new substitute for diag()
188 :    
189 :     * R/Auxiliaries.R (nnzero): fix for "diagU2N"-case
190 :     (as0, as1): new utility.
191 :    
192 :     * R/Csparse.R (diag, band): need diagU2N()
193 :    
194 :     * src/dgeMatrix.c (get_norm): return NA when 'x' slot has NA/NaN.
195 :    
196 :     * R/lMatrix.R: coerce(nMatrix |-> lMatrix) fix
197 :    
198 :     * R/Ops.R (Compare): fix <nsp> o <nsp> case
199 :    
200 :     * R/nsparseMatrix.R, R/pMatrix.R: is.na() method
201 :    
202 :     2008-04-16 Martin Maechler <maechler@stat.math.ethz.ch>
203 :    
204 :     * R/Auxiliaries.R (signPerm): new utility for
205 :     * R/Auxiliaries.R (detSparseLU): determinant() via sparseLU
206 :    
207 :     * src/dsCMatrix.c (dsCMatrix_LDL_D): suppress 'CHOLMOD warning';
208 :     since we have our own error handler (and can use tryCatch() from R).
209 :    
210 :     2008-04-15 Martin Maechler <maechler@stat.math.ethz.ch>
211 :    
212 :     * R/dgTMatrix.R (image): ha! set col=NA if lwd is small -- very nice!
213 :    
214 :     * R/dsCMatrix.R (determinant): use tryCatch() and switch to lu()
215 :     when not positive definite.
216 :    
217 :     * R/Auxiliaries.R (asTri): new auxiliary
218 :     (non0.i): make *much* faster for Tsparse with many non-zero
219 :     entries; add 'uniqT = TRUE' argument to be used when sorting is undesired.
220 :    
221 :     * tests/Class+Meth.R (dotestMat): now build on checkMatrix() from
222 :     test-tools.R , see below
223 :    
224 :     * R/dMatrix.R: fix "Summary" method: + diagU2N()
225 :    
226 :     * NAMESPACE, R/Matrix.R: add mean() method
227 :    
228 :     2008-04-12 Martin Maechler <maechler@stat.math.ethz.ch>
229 :    
230 :     * R/dgTMatrix.R (image): allow to *not* take abs(), and use
231 :     cold-hot colors; try *changed* default useAbs = FALSE
232 :     * man/image-methods.Rd: nice examples
233 :    
234 :     2008-04-11 Martin Maechler <maechler@stat.math.ethz.ch>
235 :    
236 :     * inst/test-tools.R (checkMatrix): new function for modularizing part
237 :     of tstMatrixClass() in tests/Class+Meth.R
238 :    
239 :     * R/dsCMatrix.R: coercion from "matrix"
240 :     * R/ltTMatrix.R, R/ntTMatrix.R: ditto (change it).
241 :    
242 :     * tests/Class+Meth.R (tstMatrixClass): some cleanup;
243 :     add test for as(matrix(,0,0), <class>)
244 :    
245 :     2008-04-09 Martin Maechler <maechler@stat.math.ethz.ch>
246 :    
247 :     * src/dgeMatrix.c (dgeMatrix_determinant): for n == 0,
248 :     work as determinant(matrix(,0,0)).
249 :    
250 :     * src/dgCMatrix.c (dgCMatrix_LU): return {L,U} as dtCMatrix
251 :     * man/sparseLU-class.Rd: ditto
252 :    
253 :     * R/dgCMatrix.R (determinant): method building on lu()
254 :     * R/sparseMatrix.R, Matrix.R, ...: ditto
255 :    
256 :     * R/Auxiliaries.R (mkDet): auxiliary for determinant()
257 :    
258 :     2008-04-07 Martin Maechler <maechler@stat.math.ethz.ch>
259 :    
260 :     * R/sparseMatrix.R (summary<sparseMatrix>): no 'x' column for
261 :     pattern matrices.
262 :    
263 : maechler 2166 2008-04-02 Martin Maechler <maechler@stat.math.ethz.ch>
264 :    
265 :     * src/dense.c (dense_to_Csparse): all declarations *before*
266 :     R_CheckStack(); needed e.g. for ancient gcc 2.96.
267 :    
268 :    
269 : maechler 2159 2008-03-29 Martin Maechler <maechler@stat.math.ethz.ch>
270 :    
271 :     * DESCRIPTION (Version): 0.999375-9 --- need to release
272 :     for R-devel (and R 2.7.0 alpha soon).
273 :    
274 : maechler 2165 * R/AllClass.R: drop "double" from "atomicVector" class union
275 :    
276 : maechler 2161 * R/AllGeneric.R (rcond): check for base::rcond instead of R version
277 : maechler 2164 * R/dgeMatrix.R: ditto
278 : maechler 2161
279 : maechler 2159 * R/sparseMatrix.R (summary): count NAs
280 :    
281 : maechler 2165 * inst/doc/Intro2Matrix.Rnw: changes, aim for *one* introduction.
282 :    
283 : maechler 2158 2008-03-28 Martin Maechler <maechler@stat.math.ethz.ch>
284 :    
285 :     * R/AllGeneric.R: rcond(., norm) instead of rcond(., type), in
286 :     order to become compatible to new R 2.7.0 base::rcond().
287 :    
288 : maechler 2157 2008-03-25 Martin Maechler <maechler@stat.math.ethz.ch>
289 :    
290 : maechler 2158 * DESCRIPTION (Version,Date): 0.999375-8 --- released to CRAN
291 : maechler 2157
292 :     * R/diagMatrix.R (Ops): fix newly introduce bug in <.di> o <numeric>
293 :    
294 :     * inst/test-tools.R (isValid): new utility, used much in
295 :     * tests/simple.R:
296 :    
297 :     * man/BunchKaufman-methods.Rd: added too
298 :    
299 :     2008-03-24 Martin Maechler <maechler@stat.math.ethz.ch>
300 :    
301 :     * R/dsyMatrix.R: add BunchKaufman() methods.
302 :     * R/dspMatrix.R:
303 :    
304 :     * src/init.c: add dsyMatrix_trf
305 :    
306 :     2008-03-23 Douglas Bates <bates@stat.wisc.edu>
307 :    
308 :     * DESCRIPTION (Version): release 0.999375-7
309 :     * src/CHMfactor.c (CHMfactor_update): fix
310 :    
311 : maechler 2154 2008-03-22 Martin Maechler <maechler@stat.math.ethz.ch>
312 :    
313 :     * src/dsCMatrix.c (dsCMatrix_LDL_D): cleanup, also using
314 :     internal_chm_factor().
315 :    
316 :     * R/AllGeneric.R: do *not* define a "chol" generic
317 :     (but rather use the implicit one *without* making pivot
318 :     part of the signature)
319 :     * R/*.R: drop the 'pivot' from chol's signature and make
320 :     'pivot=FALSE' a default argument of method definitions.
321 :    
322 :     * .Rbuildignore: add 'wrld_1deg': I.e. do not put it into released
323 :     version of Matrix
324 :    
325 : maechler 2139 2008-03-18 Martin Maechler <maechler@stat.math.ethz.ch>
326 :    
327 : maechler 2144 * R/Tsparse.R (.T.2.n): drop 0's before coercion to "nMatrix"
328 :    
329 :     * R/sparseMatrix.R (is.na): new simple method
330 :     * R/denseMatrix.R (is.na): ditto.
331 :    
332 :     * R/diagMatrix.R (.symDiagonal): newly exported utility.
333 :    
334 :     * R/diagMatrix.R (Ops): <diag> * <numeric> should not become dgeMatrix!
335 :    
336 : maechler 2139 * src/UFsparse_download.sh: -->
337 :     * src/CHOLMOD/: update to CHOLMOD version 1.6 (Nov.2007)
338 :    
339 : maechler 2137 2008-03-17 Martin Maechler <maechler@stat.math.ethz.ch>
340 :    
341 :     * src/dsCMatrix.c (dsCMatrix_LDL_D): even faster utility with same
342 :     functionality; barely tested in
343 :     * tests/factorizing.R
344 :    
345 :     * src/Csparse.c (diag_tC): new functionality to enable faster
346 :     determinant(<dsCMatrix>, .) in
347 :     * R/dsCMatrix.R
348 :    
349 :     2008-03-17 18:53 Douglas Bates <bates@stat.wisc.edu>
350 :    
351 :     * R/CHMfactor.R, inst/include/Matrix.h, inst/include/Matrix_stubs.c,
352 :     src/CHMfactor.c, src/CHMfactor.h,
353 :     man/CHMfactor-class.Rd, src/init.c, tests/factorizing.R:
354 :     Log-determinant of the parent matrix from a CHMfactor object as
355 :     chm_factor_ldetL2; documentation and support
356 :    
357 :     2008-03-15 Martin Maechler <maechler@stat.math.ethz.ch>
358 :    
359 :     * R/dsCMatrix.R: enable determinant(<dsCMatrix>, .) via chol(.)
360 :    
361 : maechler 2130 2008-03-14 Martin Maechler <maechler@stat.math.ethz.ch>
362 :    
363 :     * R/dsCMatrix.R: setAs(., "dsCMatrix") but with a deprecation
364 :     warning.
365 :    
366 : maechler 2128 2008-03-13 Martin Maechler <maechler@stat.math.ethz.ch>
367 :    
368 :     * DESCRIPTION (Version, Date): bug-fix release 0.999375-6
369 :    
370 :     * R/diagMatrix.R (diag2tT.u): utility to be smarter in
371 :     <diagonal> o <sparse_triangular>
372 :     setAs(., "nMatrix") added.
373 :    
374 :     * R/diagMatrix.R (Diagonal): Diagonal(4, x=3) now works too
375 :    
376 :     * R/Auxiliaries.R (.diagU2N): more careful coercion in 2 steps
377 :     new argument 'checkDense = FALSE'.
378 :    
379 :    
380 : maechler 2125 2008-03-07 Martin Maechler <maechler@stat.math.ethz.ch>
381 :    
382 : maechler 2127 * src/dgeMatrix.c (dgeMatrix_exp): fix the octave-origin bug in the
383 :     back-permutation of the matrix exponential.
384 :    
385 :     * tests/matr-exp.R: test the fix (for an example where expm() was wrong).
386 :    
387 : maechler 2126 * DESCRIPTION (Date,Version): ready to release 0.999375-5
388 :    
389 : maechler 2125 * tests/simple.R: testing diagN2U
390 :    
391 :     2008-03-06 Martin Maechler <maechler@stat.math.ethz.ch>
392 :    
393 :     * R/Auxiliaries.R (diagN2U): interface to
394 :    
395 :     * src/Csparse.c (Csparse_diagN2U): .Call()able SEXP version of chm_diagN2U()
396 :    
397 :     * tests/matprod.R: test for triangularity preserving <dtC> %*% <dtC>
398 :    
399 : maechler 2123 2008-03-05 Martin Maechler <maechler@stat.math.ethz.ch>
400 :    
401 : maechler 2125 * src/chm_common.c (chm_diagN2U): new utility.
402 :    
403 :     * src/Csparse.c (Csparse_Csparse_crossprod, Csparse_Csparse_prod):
404 :     make use of chm_diagN2U() and hence now preserve triangularity and
405 :     unit-triangularity.
406 :    
407 : maechler 2123 * DESCRIPTION (LicenseDetails): new; such that 'License:' becomes "canonical"
408 :    
409 : maechler 2120 2008-03-04 Martin Maechler <maechler@stat.math.ethz.ch>
410 :    
411 :     * R/diagMatrix.R (subDiag): fix when x[..] became a vector
412 :    
413 :     * src/Tsparse.c (Tsparse_diagU2N): new utility, necessary for e.g.
414 :     * src/Csparse.c (Csparse_crossprod): use [CT]sparse_diagU2N() !!
415 :    
416 :     * R/Auxiliaries.R (.diagU2N): make use of new Tsparse_diagU2N
417 :    
418 :     * R/Ops.R ("-" (<sparseMatrix>)): use diagU2N()
419 :    
420 :     * src/chm_common.c (AS_CHM_FINISH): add note about problem
421 :     for triangular (diag = "U").
422 :    
423 : maechler 2115 2008-02-21 Martin Maechler <maechler@stat.math.ethz.ch>
424 :    
425 :     * R/Auxiliaries.R (as_Csparse2): drop this, replacing by
426 :     * R/bind.R: .Call(dense_to_Csparse, *)
427 :    
428 :     2008-02-20 Martin Maechler <maechler@stat.math.ethz.ch>
429 :    
430 :     * R/Matrix.R (Matrix): no longer use coercions to specific classes
431 :     (since we are discouraging them in user code).
432 :    
433 :     * tests/*.R: also replaces coercions to specific classes by
434 :     coercions to super classes.
435 :    
436 :     * R/denseMatrix.R (.dense2C): simplified by using forceSymmetric()
437 :    
438 :    
439 :     2008-02-19 Martin Maechler <maechler@stat.math.ethz.ch>
440 :    
441 :     * man/CAex.Rd: example: coerce to symmetric*, not dsC*
442 :    
443 :     * src/dense.c (dense_band): generalized from ddense_band
444 :    
445 :     * R/ddenseMatrix.R (.trilDense,.triuDense, .bandDense):
446 :     now for "denseMatrix" (instead of just "ddense*"); much
447 :     simplified setMethod()s for these.
448 :    
449 :     * src/dense.c (dense_to_symmetric): generalized from ddense_*
450 :    
451 :     2008-02-18 Martin Maechler <maechler@stat.math.ethz.ch>
452 :    
453 :     * R/AllGeneric.R: forceSymmetric() generic: fast no-checking
454 :     version of as(*, "symmetricMatric").
455 :    
456 :     * src/dense.c (ddense_to_symmetric): add 'symm_test' argument, and
457 :     * R/symmetricMatrix.R: set it TRUE in coercion to "symmetricMatrix"
458 :    
459 : maechler 2113 2008-02-16 Martin Maechler <maechler@stat.math.ethz.ch>
460 :    
461 :     * R/Matrix.R (subset.ij): utility, as first step to faster
462 :     M [ <ij-matrix> ] indexing.
463 :    
464 :     * R/Matrix.R (.M.sub.i.logical): M[ <logical> ] : try better.
465 :    
466 :     * src/dense.c (ddense_symmpart, ddense_skewpart): new functions
467 :     for more efficient symmpart() and skewpart() methods.
468 :    
469 :     * src/Mutils.c (equal_string_vectors): utility
470 :    
471 :     * src/dense.c (ddense_to_symmetric): new function used in
472 :    
473 :     * R/symmetricMatrix.R: setAs(., "symmetricMatrix")
474 :    
475 :     * R/sparseMatrix.R, et_al (isSymmetric): add '...' to formals, in
476 :     order to match the generic (and evade .local(..)).
477 :    
478 :     * R/dsCMatrix.R: dgC -> dsC: use C code!
479 :    
480 :     * NAMESPACE, R/AllGeneric.R (symmpart, skewpart): new functions
481 :     as per TODO
482 :    
483 :     * R/Auxiliaries.R (setZero, all0Matrix): new utilities
484 :    
485 :     * R/symmetricMatrix.R: obvious symmpart(), skewpart() methods
486 :    
487 :    
488 :     2008-02-15 Martin Maechler <maechler@stat.math.ethz.ch>
489 :    
490 :     * R/Ops.R (.Arith.Csparse): use diagU2N when needed in triangular
491 :    
492 :     * R/Auxiliaries.R (non0.i): take out of non0ind
493 :    
494 :     * R/ddenseMatrix.R (.trilDense, .triuDense, .bandDense):
495 :     make tril(), triu(), band() work for "matrix" and all "dense*"
496 :    
497 :     * R/triangularMatrix.R (.tri[lu].tr): need .diagU2N(*)
498 :     * tests/simple.R: test the fix above
499 :    
500 :     * R/sparseMatrix.R ([): simplification: no coerce to <general>
501 :     before we use as(., <Tsparse>)[...] anyway
502 :    
503 :     * R/Rsparse.R (.viaC.to.R): mostly instead of .viaC.to.dgR()
504 :    
505 :     * R/triangularMatrix.R (isTriangular): methods for all subclasses
506 :     instead of "triangularMatrix" -- just to disambiguate
507 :    
508 :     2008-02-14 Martin Maechler <maechler@stat.math.ethz.ch>
509 :    
510 :     * tests/Class+Meth.R (dotestMat): add m[FALSE, FALSE] { <-> TODO}
511 :     * tests/indexing.R: example that fails above
512 :    
513 : maechler 2110 2008-01-26 Martin Maechler <maechler@stat.math.ethz.ch>
514 :    
515 :     * R/Matrix.R (.M.sub.i.2col): fix for logical matrix indexing
516 :     * R/Tsparse.R (.TM.sub.i.2col, .TM.repl.i.2col): ditto;
517 :     now, M[lower.tri(M)] and M[lower.tri(M)] <- v work better
518 :    
519 :     * src/Tsparse.c (Tsparse_to_tCsparse): new fast utility.
520 :     * src/Tsparse.h, init.c: ditto
521 :     * R/Auxiliaries.R (isTriT): new; faster than going via Csparse
522 :     both isTriC() and isTriT() now return TRUE with "kind" or FALSE.
523 :     * R/sparseMatrix.R (isTriangular): hence simplified
524 :    
525 : maechler 2108 2008-01-24 Martin Maechler <maechler@stat.math.ethz.ch>
526 :    
527 :     * R/Ops.R (.Arith.Csparse): new utility factored out of former
528 :     <dgC> o <dgC>, extended for triangular and also used in <dtC> o <dtC>.
529 :    
530 : maechler 2106 2008-01-23 Martin Maechler <maechler@stat.math.ethz.ch>
531 :    
532 :     * tests/factorizing.R (checkSchur): and more tests for checking Schur()
533 :    
534 : maechler 2108 * inst/test-tools.R (isOrthogonal): new function; also file restructured
535 : maechler 2106
536 :     2008-01-22 Martin Maechler <maechler@stat.math.ethz.ch>
537 :    
538 :     * R/ngTMatrix.R: allow as(<numeric matrix>, "ngTMatrix") and hence
539 :     coercion to "nMatrix" and "pMatrix"
540 :    
541 :     * R/AllClass.R: "Schur" class; "number" class union
542 :     * man/number-class.Rd:
543 :     * man/Schur-class.Rd:
544 :    
545 :     * R/eigen.R (.dgeSchur): utility, and return "Schur" class
546 :     (.simpleSchur): Schur() method for diagonal matrices
547 :     (.triSchur): Schur() method for triangular matrices
548 :     (Schur.sym): Schur() for symmetric matrices {building on eigen()}.
549 :    
550 :    
551 :     2008-01-21 Martin Maechler <maechler@stat.math.ethz.ch>
552 :    
553 :     * src/dgCMatrix.c (dgCMatrix_QR): set @Dim slot (as per doc)
554 :    
555 : maechler 2105 2008-01-15 Martin Maechler <maechler@stat.math.ethz.ch>
556 :    
557 :     * R/CHMfactor.R (solve): method for b="numeric", but also b="ANY"
558 :     in order to ensure 'system = *' is not lost;
559 :     formals()$system instead of cut&paste.
560 :     * tests/factorizing.R: test solve(<CHM..>, <numeric>)
561 :    
562 : maechler 2102 2008-01-11 Martin Maechler <maechler@stat.math.ethz.ch>
563 : maechler 2096
564 : maechler 2105 * DESCRIPTION (Date): make ready for release --> 0.999375-4
565 : maechler 2096
566 : maechler 2102 * R/dgeMatrix.R: fix rcond() method for "dgeMatrix".
567 : maechler 2096
568 : maechler 2098 2007-12-08 Martin Maechler <maechler@stat.math.ethz.ch>
569 : maechler 2096
570 : maechler 2098 * R/pMatrix.R: as(*, "matrix") now returns 0/1 *integer* matrix,
571 :     and hence does as.vector(.).
572 :     * man/pMatrix-class.Rd: docs
573 :     * R/sparseMatrix.R: fix for printing "integer sparse"
574 :    
575 :     * tests/Class+Meth.R (tstMatrixClass): test M[FALSE], M[2] etc
576 :    
577 :     * R/Matrix.R and others: use "exact" function argument list for
578 :     both "[" : (x, i,j, ..., drop)
579 :     and "[<-" : (x, i,j, ..., value)
580 :    
581 :     * R/denseMatrix.R: M[i] and M[i] <- v (i vector) now work
582 :     * R/Tsparse.R (replTmat): ditto
583 :     * R/diagMatrix.R (replDiag): ditto
584 :     * R/Csparse.R (replCmat): ditto {was it worth the pain?}
585 :     * tests/indexing.R: testing the above
586 :    
587 : maechler 2096 2007-12-07 Martin Maechler <maechler@stat.math.ethz.ch>
588 :    
589 :     * R/sparseMatrix.R (cov2cor): method for sparse matrices
590 :    
591 :     * R/diagMatrix.R ([<-): fix D[ cbind(i,j) ] <- v
592 :    
593 :     * R/bind2.R: fix for Rsparse* and rbind2(dense,dense)
594 :    
595 :     * tests/Class+Meth.R: test cbind2, rbind2 and diag<-
596 :    
597 :     2007-12-06 Martin Maechler <maechler@stat.math.ethz.ch>
598 :    
599 :     * R/Matrix.R: "generic" cov2cor() method
600 :    
601 :     * R/nearPD.R: new 'only.values', 'keepDiag' arguments;
602 :     speed up Q %*% D %*% t(Q)
603 :     * tests/dpoMatrix.R: test nearPD()
604 :    
605 :     2007-12-05 Doug Bates and Martin Maechler
606 :    
607 :     * R/sparseMatrix.R: xtabs(*, sparse=.) function; an extention of
608 :     stats::xtabs() allowing to create sparse matrices.
609 :    
610 :     2007-10-08 Martin Maechler <maechler@stat.math.ethz.ch>
611 :    
612 :     * DESCRIPTION (Version): *-4 (released *-3 two days ago)
613 :    
614 : maechler 2081 2007-10-06 Martin Maechler <maechler@stat.math.ethz.ch>
615 :    
616 :     * R/pMatrix.R: solve(<Matrix>, <pMatrix>)
617 :    
618 :     2007-10-05 Martin Maechler <maechler@stat.math.ethz.ch>
619 :    
620 :     * R/LU.R: solve() method for "denseLU"
621 :    
622 :     2007-10-01 Martin Maechler <maechler@stat.math.ethz.ch>
623 :    
624 :     * DESCRIPTION (Version): 0.999375-3 preparing for release
625 :    
626 :     * R/AllGeneric.R: simplify if(.) .. else .. for R <= 2.5.1
627 :    
628 :     * R/Matrix.R (Matrix): .Internal(matrix(..)) different for R >= 2.7.0
629 :    
630 : maechler 2073 2007-09-26 Martin Maechler <maechler@stat.math.ethz.ch>
631 :    
632 :     * R/pMatrix.R (.m.mult.pMat): fix <matrix> %*% <pMatrix>,
633 :     thanks to Kasper Kristensen.
634 :     * tests/matprod.R: regression test for that.
635 :    
636 : bates 2069 2007-09-23 17:32 Douglas Bates <bates@stat.wisc.edu>
637 :    
638 :     * [r4778] R/AllGeneric.R: Check R version before defining generics for
639 :     primitives
640 :    
641 : maechler 2073 2007-09-13 Martin Maechler <maechler@stat.math.ethz.ch>
642 :    
643 :     * R/denseMatrix.R (rcond): method
644 :     * R/sparseQR.R (rcond): method, use x or t(x)
645 :    
646 :     2007-09-12 Martin Maechler <maechler@stat.math.ethz.ch>
647 :    
648 :     * R/dgeMatrix.R (rcond): method: work via qr.R() for non-square
649 :     matrices.
650 :     * R/sparseMatrix.R: Ditto for all other rcond() method definitions.
651 :    
652 :     * man/rcond.Rd: mention the more general definition, and add
653 :     example for non-square matrices.
654 :    
655 :     * man/chol.Rd: new file, for the S4 chol() generic and all methods.
656 :    
657 :     2007-09-11 Martin Maechler <maechler@stat.math.ethz.ch>
658 :    
659 :     * R/sparseQR.R: add qr.R() method [to be used for rcond()]
660 :    
661 : maechler 2062 2007-09-01 Martin Maechler <maechler@stat.math.ethz.ch>
662 :    
663 :     * R/Matrix.R ([<-): add (Matrix,missing,ANY,Matrix) etc
664 :     * tests/indexing.R: add new regression for the above cases.
665 :    
666 : maechler 2061 2007-08-30 Martin Maechler <maechler@stat.math.ethz.ch>
667 :    
668 :     * src/Mutils.h (__sun): clause for alloca.h on Solaris
669 :    
670 : maechler 2056 2007-08-16 Martin Maechler <maechler@stat.math.ethz.ch>
671 :    
672 :     * DESCRIPTION (Date, Version): 0.999375-2
673 :    
674 :     2007-08-15 Martin Maechler <maechler@stat.math.ethz.ch>
675 :    
676 :     * R/HBMM.R (readMM): make work for pattern matrices as well
677 :    
678 : bates 2050 2007-08-14 13:07 Douglas Bates <bates@stat.wisc.edu>
679 :    
680 :     * [r4730] src/Mutils.h: declare alloca
681 :     * [r4734] NAMESPACE, R/AllGeneric.R, R/Csparse.R, R/HBMM.R, R/Tsparse.R,
682 :     R/dgCMatrix.R, R/dgTMatrix.R, R/dsCMatrix.R, R/dsTMatrix.R,
683 :     man/externalFormats.Rd, src/Csparse.c, src/Csparse.h, src/DEPS.mkf,
684 :     src/HBMM.c, src/HBMM.h, src/Mutils.h, src/SOURCES_C.mkf, src/init.c,
685 :     src/mmio.c, src/mmio.h: Remove deprecated function writeHB and its
686 :     methods; switch writeMM to use CHOLMOD code; repair readMM
687 :    
688 : maechler 2048 2007-08-14 Martin Maechler <maechler@stat.math.ethz.ch>
689 :    
690 :     * R/nearPD.R, man/nearPD.Rd (nearPD): new function built on Jens
691 :     Oehlschlaegel's ... result type still to be discussed!
692 :    
693 : maechler 2043 2007-08-10 Martin Maechler <maechler@stat.math.ethz.ch>
694 :    
695 :     * man/image-methods.Rd: new, combining all image() methods
696 :    
697 :     2007-08-09 Martin Maechler <maechler@stat.math.ethz.ch>
698 :    
699 :     * R/dgCMatrix.R: define qr() and lu() methods for "sparseMatrix"
700 :     to work via dgC...
701 :    
702 :     * R/Matrix.R (Matrix): special treatment for "table" (S3)
703 :    
704 :     2007-08-07 Martin Maechler <maechler@stat.math.ethz.ch>
705 :    
706 :     * R/dgTMatrix.R (image): change defaults to
707 :     aspect = "iso", colorkey = FALSE
708 :    
709 : maechler 2039 2007-08-06 Martin Maechler <maechler@stat.math.ethz.ch>
710 :    
711 :     * src/dsyMatrix.c (dsyMatrix_matrix_mm): 'b' might be matrix;
712 :     must copy its *expanded* x slot before LAPACK call.
713 :    
714 :     * tests/matprod.R: test the last days' changes.
715 :    
716 : bates 2041 2007-08-06 16:43 Douglas Bates <bates@stat.wisc.edu>
717 :    
718 :     * [r4712] inst/include/Matrix_stubs.c: Change R_cholmod_printf in stubs
719 :     as well as in sources
720 : bates 2050 * [r4713] src/dsyMatrix.c: Duplicate the contents of the RHS before
721 :     Lapack call
722 : maechler 2043
723 : maechler 2036 2007-08-03 Martin Maechler <maechler@stat.math.ethz.ch>
724 :    
725 :     * R/Matrix.R (%*%, crossprod, tcrossprod): add method for
726 : maechler 2039 ("Matrix", "matrix") which is needed in some cases.
727 :     Ditto for solve().
728 : maechler 2036
729 :     * R/colSums.R (.as.dge.Fun): need ddenseMatrix methods to avoid
730 :     infinite recursion in dispatch for some cases.
731 :    
732 : bates 2041 2007-08-02 08:48 Martin Maechler <maechler@stat.math.ethz.ch>
733 : maechler 2036
734 : bates 2041 * [r4693] src/chm_common.c: R_cholmod_printf() instead of Rprintf() just
735 :     so pointers match
736 :    
737 : maechler 2024 2007-08-02 Martin Maechler <maechler@stat.math.ethz.ch>
738 :    
739 : maechler 2036 * DESCRIPTION (Date): set ready for release -- 0.999375-1
740 : maechler 2024
741 : bates 2020 2007-08-01 15:44 Douglas Bates <bates@stat.wisc.edu>
742 :    
743 :     * [r4686] inst/include/Matrix.h, inst/include/Matrix_stubs.c,
744 :     src/chm_common.c, src/chm_common.h: Change API for
745 :     numeric_as_chm_dense and N_AS_CHM_DN
746 : maechler 2024
747 : maechler 2018 2007-08-01 Martin Maechler <maechler@stat.math.ethz.ch>
748 :    
749 :     * src/dtrMatrix.c (dtrMatrix_matrix_mm): fix dimensionality check (!)
750 :     * tests/matprod.R: regr.test for it
751 :    
752 : maechler 2011 2007-07-20 Martin Maechler <maechler@stat.math.ethz.ch>
753 :    
754 :     * R/dMatrix.R: fix from Brian for Math2(., digits = "missing")
755 :     * tests/group-methods.R: and regression-test it
756 :    
757 : bates 2008 2007-07-19 19:45 Douglas Bates <bates@stat.wisc.edu>
758 :    
759 :     * [r4642] inst/include/Matrix.h, inst/include/Matrix_stubs.c,
760 :     inst/include/cholmod.h, src/chm_common.c, src/init.c: Export
761 :     triplet_to_sparse, documentation, use typedefs
762 : maechler 2011
763 : maechler 2005 2007-07-18 Martin Maechler <maechler@stat.math.ethz.ch>
764 :    
765 :     * man/dpoMatrix-class.Rd: added 'corMatrix' example
766 :    
767 :     * src/dsyMatrix.[ch] (dsyMatrix_as_matrix): new 'keep_dimnames' arg
768 :     * src/dtrMatrix.[ch] (dtrMatrix_as_matrix): ditto
769 :     * src/init.c, R/dsyMatrix.R, R/dtrMatrix.R, R/lgTMatrix.R: ditto
770 :    
771 :     * R/lsparseMatrix.R: bug fix in "all" method
772 :     * R/Ops.R (.do.Logic.lsparse): "|" bug in borderline case
773 :    
774 :     * R/dsyMatrix.R (coerce->dsTMatrix): (i,j) slots should *not* have names
775 :     * R/ngTMatrix.R (coerce->ngTMatrix): ditto;
776 :     + matrix |-> nMatrix coercion
777 :     * R/pMatrix.R: + setAs() to dMatrix and from nMatrix
778 :     * man/pMatrix-class.Rd: ditto
779 :    
780 :     * R/Matrix.R (Summary): method for non-dMatrix
781 :    
782 :     * tests/Class+Meth.R (extraValid): new check about "dirty" slots
783 :     * tests/Class+Meth.R (tstMatrixClass): test norm(.);
784 :     test all Summary methods.
785 :    
786 :     2007-07-16 Martin Maechler <maechler@stat.math.ethz.ch>
787 :    
788 :     * R/dgeMatrix.R (norm, rcond): methods for 'matrix'
789 :    
790 :     2007-07-14 Martin Maechler <maechler@stat.math.ethz.ch>
791 :    
792 :     * R/sparseMatrix.R (norm): simple methods for sparseMatrix
793 :    
794 :     * R/pMatrix.R (t?crossprod): methods for pMatrix
795 :    
796 : bates 1987 2007-07-10 Douglas Bates <bates@stat.wisc.edu>
797 :    
798 :     * src/dgeMatrix.c (dgeMatrix_colsums): Get the logic straight.
799 :    
800 : bates 1975 2007-07-09 20:45 Douglas Bates <bates@stat.wisc.edu>
801 :    
802 :     * [r4579] src/dgeMatrix.c: Untangle horrible code in dgeMatrix_colsums
803 : maechler 2005 trying to fix a subtle bug - which has been somewhere else.
804 : bates 1975
805 :     2007-07-09 19:43 Martin Maechler <maechler@stat.math.ethz.ch>
806 :    
807 :     * [r4578] src/dgeMatrix.c: "cleaned" dgeMatrix_colsums() - but did not
808 :     solve the bug
809 :    
810 : maechler 1968 2007-07-08 Martin Maechler <maechler@stat.math.ethz.ch>
811 : bates 1964
812 : maechler 1968 * src/dgCMatrix.c (compressed_to_TMatrix):
813 :    
814 :     2007-07-07 Martin Maechler <maechler@stat.math.ethz.ch>
815 :    
816 :     * src/Csparse.c (Rsparse_validate): new, to have some validity
817 :     checking for RsparseMatrix
818 :     * src/dgCMatrix.c (xRMatrix_validate): ditto
819 :     * src/dtCMatrix.c (tRMatrix_validate): ditto
820 :    
821 :     2007-07-07 Douglas Bates <bates@stat.wisc.edu>
822 :    
823 : bates 1964 * [r4567] R/AllClass.R: Slots already in RsparseMatrix were redefined in
824 :     lgRMatrix
825 :     * [r4568] DESCRIPTION: Prepare for bug-fix release
826 : bates 1966 * [r4570] src/CHOLMOD/Check/cholmod_write.c: Include cholmod_matrixops.h
827 :     for declaration of cholmod_symmetry
828 : maechler 1968
829 : maechler 1961 2007-07-06 Martin Maechler <maechler@stat.math.ethz.ch>
830 :    
831 :     * DESCRIPTION (Version): 0.999375 merged into the trunk; ready for
832 :     release.
833 :    
834 : maechler 1960 2007-07-06 14:11 Douglas Bates <bates@stat.wisc.edu>
835 :    
836 :     * [r4559] src/iohb.c, src/iohb.h: Remove Harwell-Boeing input/output
837 :     functions - no longer used
838 :     * [r4560] src/HBMM.c, src/Mutils.c, src/dgTMatrix.c, src/dgeMatrix.c,
839 :     src/dspMatrix.c, src/dsyMatrix.c, src/dtCMatrix.c,
840 :     src/factorizations.c, src/sparseQR.c: Replace most calls to Calloc by
841 :     Alloca
842 :    
843 :     2007-07-06 13:14 Martin Maechler <maechler@stat.math.ethz.ch>
844 :    
845 :     * [r4558] inst/doc/Comparisons.Rnw, src/CHMfactor.c, src/Csparse.c,
846 :     src/Tsparse.c, src/chm_common.c, src/chm_common.h, src/dense.c,
847 :     src/dgCMatrix.c, src/dsCMatrix.c, src/dtTMatrix.c, src/sparseQR.c,
848 :     src/t_gCMatrix_colSums.c: more R_CheckStack()s
849 :    
850 :     2007-07-05 18:12 Douglas Bates <bates@stat.wisc.edu>
851 :    
852 :     * [r4550] inst/include/Matrix.h: Add the macro N_AS_CHM_DN to "alloca"
853 :     the required amount of memory then call M_numeric_as_chm_dense.
854 :     * [r4556] src/Mutils.h, src/dgCMatrix.c: Define and use the Alloca macro
855 :     (like Calloc but calling alloca)
856 :    
857 : maechler 1947 2007-07-05 Martin Maechler <maechler@stat.math.ethz.ch>
858 :    
859 :     * R/sparseMatrix.R (printSpMatrix): renamed from prSpMatrix()
860 :     and extended with more sophisticated 'col.names' option.
861 :     * NAMESPACE: export printSparseMatrix()
862 :     * man/printSpMatrix.Rd: document, incl. examples
863 :    
864 : maechler 1960 2007-07-04 16:21 Douglas Bates <bates@stat.wisc.edu>
865 :    
866 :     * [r4543] src/cs_utils.c, src/cs_utils.h, src/dgCMatrix.c,
867 :     src/dtCMatrix.c, src/sparseQR.c: CSP typedef for *cs and macro
868 :     AS_CSP. API change - pass the empty structure to Matrix_as_cs.
869 :    
870 : maechler 1945 2007-07-04 Martin Maechler <maechler@stat.math.ethz.ch>
871 :    
872 :     * DESCRIPTION (Version): 0.99875-4
873 :    
874 :     * tests/Class+Meth.R (tstMatrixClass): add dimnames, and hence test
875 :     some dimnames perservation.
876 :    
877 :     * R/dsTMatrix.R (t-method): keep dimnames
878 :     * R/dtTMatrix.R: ditto
879 :    
880 :     * R/sparseMatrix.R (prSpMatrix): print colnames when non-trivial
881 :     and ncol(.) < 10
882 :    
883 :     * src/cs_utils.c: drop check_class() and use Matrix_check_class()
884 :     from Mutils.h
885 :    
886 :     * src/lgCMatrix.c ([ln]csc_to_matrix): no longer lose dimnames,
887 :     e.g. in as(<ngCMatrix>, "matrix")
888 :    
889 : maechler 1960 2007-07-01 13:27 Douglas Bates <bates@stat.wisc.edu>
890 :    
891 :     * [r4529] .: Create a branch for the API changes from the 0.99875
892 :     series to the 0.999375 series
893 :     * [r4530] DESCRIPTION, inst/include/Matrix.h,
894 :     inst/include/Matrix_stubs.c, src/CHMfactor.c, src/Csparse.c,
895 :     src/Mutils.h, src/Tsparse.c, src/chm_common.c, src/chm_common.h,
896 :     src/dense.c, src/dgCMatrix.c, src/dsCMatrix.c, src/dtTMatrix.c,
897 :     src/t_gCMatrix_colSums.c: API change - pass the empty structure to the
898 :     as_cholmod_x functions
899 :    
900 :     2007-06-30 09:05 Martin Maechler <maechler@stat.math.ethz.ch>
901 :    
902 :     * [r4527] trunk/Matrix/DESCRIPTION, trunk/Matrix/NAMESPACE,
903 :     trunk/Matrix/inst/doc/Comparisons.Rnw: add session- and hardware-info
904 :     to Comparisons
905 :    
906 :     >>>>>>> .merge-right.r4561
907 : maechler 1932 2007-06-29 Martin Maechler <maechler@stat.math.ethz.ch>
908 :    
909 :     * DESCRIPTION (Version): 0.99875-3 ready to be released.
910 :    
911 :     * R/sparseMatrix.R (spMatrix): make spMatrix(3,4) working
912 :    
913 :     * R/AllGeneric.R: set "Math" (and "Math2") group generics in a way
914 :     that should also work in a future version of R.
915 :    
916 : maechler 1922 2007-06-21 Martin Maechler <maechler@stat.math.ethz.ch>
917 :    
918 :     * NAMESPACE, R/AllClass.R: "xsparseVector" class union.
919 :    
920 :     * R/sparseVector.R: more *sparseVector coercions, notably for
921 :     non - double ones.
922 :    
923 : maechler 1911 2007-06-19 Martin Maechler <maechler@stat.math.ethz.ch>
924 :    
925 :     * R/colSums.R: new file for all (col|row)(Sums|Means) methods,
926 :     notably the new ones building on the new .Call(.)s:
927 :    
928 :     * src/dgCMatrix.c (DEF_gCMatrix_COLSUMS): use to define
929 :     all 4 of [dlin]gCMatrix_colSums().
930 :    
931 : bates 1909 2007-06-18 16:12 Douglas Bates <bates@stat.wisc.edu>
932 :    
933 :     * [r4472] src/Syms.h, src/init.c: Added Matrix_lengthSym
934 :     * [r4473] src/dgCMatrix.c: Modified dgCMatrix_colSums for sparseVector
935 :     result
936 : maechler 1911
937 : maechler 1903 2007-06-16 Martin Maechler <maechler@stat.math.ethz.ch>
938 :    
939 : maechler 1904 * R/kronecker.R: fix typo (could lead to inf.recursion)
940 :     * test/simple.R: testing that
941 :    
942 : maechler 1903 * R/sparseMatrix.R (prSpMatrix): change to be used as print()
943 : maechler 1922 method as well (which can have arguments, show() can't).
944 : maechler 1903
945 : bates 1902 2007-06-16 15:52 Douglas Bates <bates@stat.wisc.edu>
946 :    
947 :     * [r4466] R/dgCMatrix.R, src/dgCMatrix.c, src/dgCMatrix.h, src/init.c:
948 :     added dgCMatrix_colSums for [col,row][Sums,Means]
949 :    
950 : bates 1899 2007-06-15 23:15 Douglas Bates <bates@stat.wisc.edu>
951 : bates 1897
952 :     * [r4460] R/sparseMatrix.R, man/dgCMatrix-class.Rd, src/dgCMatrix.c,
953 :     src/dgCMatrix.h, src/init.c: added lm.fit.sparse (unexported),
954 :     coercion of "factor" to "dgCMatrix" and dgCMatrix_cholsol
955 :     * [r4461] R/AllClass.R, man/sparseMatrix-class.Rd: draft "indicators"
956 :     class
957 : bates 1899 * [r4463] R/sparseMatrix.R, man/dgCMatrix-class.Rd,
958 :     man/sparseMatrix-class.Rd: Don't need an "indicators" class - use the
959 :     row names to store the levels - duh! Added an example.
960 : maechler 1903
961 : maechler 1893 2007-06-14 Martin Maechler <maechler@stat.math.ethz.ch>
962 :    
963 :     * src/Csparse.c (Csparse_validate): check for *repeated* entries
964 :     thanks to example from Christian Buchta; with a test here:
965 :     * tests/simple.R:
966 :    
967 : maechler 1886 2007-06-07 Martin Maechler <maechler@stat.math.ethz.ch>
968 :    
969 :     * R/Auxiliaries.R (callGeneric): another fix, needed for some cases
970 :     of colSums(*, sparseResult = TRUE)
971 :    
972 : maechler 1883 2007-06-06 Martin Maechler <maechler@stat.math.ethz.ch>
973 :    
974 :     * R/lsparseMatrix.R, R/ldenseMatrix.R (all, any): change default to
975 :     'na.rm = FALSE' as "everywhere" else in R.
976 :    
977 : bates 1877 2007-06-05 Douglas Bates <bates@stat.wisc.edu>
978 :    
979 : bates 1878 * [r4421] src/CSparse_install.sh: Modify for new organization of
980 : maechler 1883 CSparse package
981 : bates 1877 * [r4425] src/UFsparse_download.sh: Update to version 3.0.0 of
982 :     SuiteSparse
983 :     * [r4426] src/Makefile: add ./UFconfig to the include path for
984 :     compilation
985 : maechler 1883 * [r4427] src/cs.[ch]: update to CSparse version 2.2.0
986 :     * [r4428] inst/doc/UFsparse/* src/{AMD,CHOLMOD,COLAMD}/*
987 :     src/UFconfig/UFconfig.h: Update to version 3.0.0 of SuiteSparse
988 :    
989 : maechler 1870 2007-06-05 Martin Maechler <maechler@stat.math.ethz.ch>
990 :    
991 :     * R/Auxiliaries.R (emptyColnames): + argument msg.if.not.empty, used in
992 :     * R/sparseMatrix.R (prSpMatrix): now gives a message about
993 :     suppressed column names.
994 :    
995 : bates 1868 2007-06-04 17:13 Douglas Bates <bates@stat.wisc.edu>
996 :    
997 :     * [r4418] src/Csparse.c, src/HBMM.c, src/Mutils.c, src/Mutils.h,
998 :     src/Tsparse.c, src/chm_common.c, src/chm_common.h, src/dgCMatrix.c,
999 :     src/dgeMatrix.c, src/dpoMatrix.c, src/dpoMatrix.h, src/dppMatrix.c,
1000 :     src/dppMatrix.h, src/dsCMatrix.c, src/dspMatrix.c, src/dspMatrix.h,
1001 :     src/dsyMatrix.c, src/dsyMatrix.h, src/dtpMatrix.c, src/dtrMatrix.c:
1002 :     Remove warnings after change to const char* CHAR
1003 :    
1004 :     2007-06-04 17:11 Douglas Bates <bates@stat.wisc.edu>
1005 :    
1006 :     * [r4417] inst/include/Matrix_stubs.c, inst/include/cholmod.h: Corrected
1007 :     type of M_cholmod_ssmult
1008 :    
1009 : bates 1863 2007-06-03 14:42 Douglas Bates <bates@stat.wisc.edu>
1010 :    
1011 :     * [r4412] inst/include/Matrix_stubs.c, inst/include/cholmod.h,
1012 :     src/init.c: Yet another cholmod export - cholmod_ssmult
1013 :    
1014 : maechler 1855 2007-05-23 Martin Maechler <maechler@stat.math.ethz.ch>
1015 :    
1016 :     * NAMESPACE: exported drop0(), since
1017 :     * man/drop0.Rd: I have seen several cases, I really wanted to use
1018 :     it, so our users may want too.
1019 :    
1020 :     2007-05-22 Martin Maechler <maechler@stat.math.ethz.ch>
1021 :    
1022 :     * man/colSums.Rd: separately document colSums() etc, since these
1023 :     have the extra argument 'sparseResult'.
1024 :    
1025 : maechler 1852 2007-05-21 Martin Maechler <maechler@stat.math.ethz.ch>
1026 :    
1027 :     * R/sparseMatrix.R (spMatrix): utility (T)sparse Matrix constructor;
1028 :     * man/spMatrix.Rd: docu., including examples
1029 :    
1030 :     * R/Auxiliaries.R (sp.colMeans): etc, using a patched callGeneric(),
1031 :     in order to make colMeans() etc fast *and* correct.
1032 :     * R/sparseVector.R (replSPvec): "[<-" functionality for
1033 :     sparseVectors; tested in
1034 :     * tests/simple.R:
1035 :    
1036 :     2007-05-19 Martin Maechler <maechler@stat.math.ethz.ch>
1037 :    
1038 :     * R/sparseMatrix.R (print.sparseSummary): and summary() method for
1039 :     (very) sparse Matrices; output similar to Matlab's print().
1040 :    
1041 : bates 1847 2007-05-17 Douglas Bates <bates@stat.wisc.edu>
1042 :    
1043 :     * src/HBMM.c (Matrix_writeMatrixMarket): Write 1-based, not
1044 :     0-based, indices (Jose Quesada <quesada@gmail.com>).
1045 :    
1046 : bates 1844 2007-05-16 Douglas Bates <bates@stat.wisc.edu>
1047 :    
1048 :     * R/CHMfactor.R: Added solve methods for a CHMfactor object.
1049 :    
1050 : maechler 1845 2007-05-16 Martin Maechler <maechler@stat.math.ethz.ch>
1051 :    
1052 :     * R/Auxiliaries.R (sparsapply): new utility, much faster than
1053 :     tapply1() for large sparse matrices.
1054 :    
1055 :     2007-05-15 Martin Maechler <maechler@stat.math.ethz.ch>
1056 :    
1057 :     * R/Matrix.R (dim<-): reshape now via sparseVector.
1058 :    
1059 :     * R/sparseVector.R: methods and function for
1060 :     * R/AllClass.R: new "sparseVector" class and daughters.
1061 :     * NAMESPACE: export new classes
1062 :    
1063 : maechler 1837 2007-05-14 Martin Maechler <maechler@stat.math.ethz.ch>
1064 :    
1065 :     * DESCRIPTION (Version): 0.99875-1
1066 :     * src/Makefile.win: also remove Lapack code from here (cf. 04-25).
1067 :    
1068 : maechler 1834 2007-05-11 Martin Maechler <maechler@stat.math.ethz.ch>
1069 :    
1070 :     * R/Tsparse.R ([, Tsparse): fix last case: *duplicated*, symmetric
1071 :     indexing
1072 :     * tests/indexing.R: test set for that.
1073 :    
1074 : maechler 1833 2007-05-08 Martin Maechler <maechler@stat.math.ethz.ch>
1075 :    
1076 :     * R/Tsparse.R (replTmat): fix the case of *duplicated* index
1077 :     entries.
1078 :     * tests/indexing.R(out): add regression test for it
1079 :    
1080 :     2007-04-30 Martin Maechler <maechler@stat.math.ethz.ch>
1081 :    
1082 :     * R/(l(dense|sparse))?Matrix.R (!): use 'x', not 'e1' as argument
1083 :     name for "!" method definitions.
1084 :    
1085 : maechler 1829 2007-04-26 Martin Maechler <maechler@stat.math.ethz.ch>
1086 :    
1087 :     * R/Tsparse.R (intI): new utility, used for "[" :
1088 :     Cleanup up there, and fixes for duplicated indices - more TODO!
1089 :    
1090 :     * tests/indexing.R(out): more tests
1091 :    
1092 : bates 1827 2007-04-25 Douglas Bates <bates@stat.wisc.edu>
1093 :    
1094 :     * DESCRIPTION,src/Makefile: require R>= 2.5.0 and remove Lapack
1095 :     code that is now part of the R Lapack library.
1096 : maechler 1829
1097 : bates 1827 * src/init.c,inst/include/{Matrix_stubs.c,cholmod.h}:export
1098 :     cholmod_factorize_p (used in lme4 for GLMMs and NLMMs).
1099 :    
1100 : maechler 1829 2007-04-21 Martin Maechler <maechler@stat.math.ethz.ch>
1101 :    
1102 :     * R/Matrix.R (image): method for all Matrices, not just sparse ones.
1103 :    
1104 :     2007-04-17 Martin Maechler <maechler@stat.math.ethz.ch>
1105 :    
1106 :     * R/Auxiliaries.R (tapply1): unname(.) -> colSums() etc don't end
1107 :     up with extraneous names '0'...'<n-1>'
1108 :    
1109 : maechler 1825 2007-04-12 Martin Maechler <maechler@stat.math.ethz.ch>
1110 :    
1111 :     * R/dgTMatrix.R (mat2dgT): care about NAs
1112 :    
1113 :     2007-04-11 Martin Maechler <maechler@stat.math.ethz.ch>
1114 :    
1115 :     * R/kronecker.R: triangularity preserving methods
1116 :    
1117 : maechler 1803 2007-03-27 Martin Maechler <maechler@stat.math.ethz.ch>
1118 :    
1119 :     * R/kronecker.R: new file collecting kronecker() methods in one
1120 :     place. Goal: become much faster!
1121 :    
1122 : maechler 1799 2007-03-23 Martin Maechler <maechler@stat.math.ethz.ch>
1123 :    
1124 :     * src/dtCMatrix.c (dtCMatrix_solve): use the new code from Kasper
1125 :     Kristensen based cs_spsolve() instead of _lsolve & _usolve which
1126 :     can be much faster.
1127 :    
1128 :     * tests/matprod.R: add regression tests for these (upper & lower).
1129 :    
1130 :     2007-03-19 Martin Maechler <maechler@stat.math.ethz.ch>
1131 :    
1132 :     * R/Matrix.R (diff): method for our Matrices.
1133 :    
1134 :     * R/sparseMatrix.R (isDiagonal): check dim()!
1135 :    
1136 :     2007-03-17 Martin Maechler <maechler@stat.math.ethz.ch>
1137 :    
1138 :     * R/Matrix.R (dim<-): new method for "reshape()" built on a
1139 :     proposal from Tamas Papp.
1140 :    
1141 :     2007-03-16 Martin Maechler <maechler@stat.math.ethz.ch>
1142 :    
1143 :     * R/AllGeneric.R: remove all if(!isGeneric(.)) clauses
1144 :    
1145 :     * R/zzz.R (.onLoad, .onUnload): do *not* leave bind_activation(TRUE);
1146 : maechler 1803 rather define and export cBind() and rBind() only.
1147 :     --> useRs *must* change code that used to have cbind()/rbind() !!
1148 : maechler 1799
1149 : maechler 1803 * R/bind.R: change tests from cbind() to cBind() and similarly to rBind()
1150 :     * R/bind.Rout.save: ditto
1151 : maechler 1799
1152 : bates 1787 2007-02-16 Douglas Bates <bates@r-project.org>
1153 :    
1154 :     * DESCRIPTION (Date, Version): 0.9975-11 with new date
1155 :     * src/dgCMatrix.c (R_to_CMatrix, compressed_to_TMatrix): remove
1156 :     const modifier on declaration of the array 'valid'
1157 :    
1158 : bates 1786 2007-02-12 Douglas Bates <bates@stat.wisc.edu>
1159 :    
1160 :     * R/CHMfactor.R: Add image method (coercion to sparseMatrix).
1161 :    
1162 : maechler 1765 2007-02-05 Martin Maechler <maechler@stat.math.ethz.ch>
1163 :    
1164 : maechler 1768 * DESCRIPTION (Date, Version): 0.9975-10 with new date.
1165 :    
1166 : maechler 1767 * R/Ops.R (Arith): make sure Csparse o Csparse also works for e.g. ntCMatrix
1167 :     * tests/simple.R: test the above and some of these coercions:
1168 :    
1169 :     * R/nsparseMatrix.R: coercing "Csparse" to "lsparseMatrix";
1170 :     be careful to avoid infinite recursion, using new coercions in
1171 :     * R/ngCMatrix.R and nsC... and ntC...
1172 :     * R/lsparseMatrix.R: ditto
1173 :    
1174 : maechler 1765 * R/SparseM-conv.R: more conversion, notably for triplet matrices.
1175 :    
1176 : maechler 1767 * src/dgCMatrix.c (R_to_C_Matrix): port Doug's fix and
1177 :     * R/Rsparse.R: reactivate .Call()s
1178 : maechler 1765
1179 : maechler 1767 * tests/Class+Meth.R: a bit more on actual classes
1180 :    
1181 :     2007-02-04 Douglas Bates <bates@stat.wisc.edu>
1182 :    
1183 :     * src/dgCMatrix.c (compressed_to_TMatrix): fix memory bug using strdup()
1184 :    
1185 : maechler 1760 2007-02-03 Martin Maechler <maechler@stat.math.ethz.ch>
1186 : maechler 1758
1187 :     * DESCRIPTION (Version): 0.9975-10 to upload
1188 :    
1189 : maechler 1760 * tests/Class+Meth.R (tstMatrixClass): require coercions to
1190 :     specific classes less unconditionally.
1191 :    
1192 :     * R/Auxiliaries.R: get rid of as_Tsparse() and as_Rsparse()
1193 :    
1194 :     * R/Tsparse.R (triu): etc, use as(*, "TsparseMatrix") instead of as_Tsparse()
1195 :    
1196 :     * R/Rsparse.R (.R.2.T): R-level workaround using compressed_to_TMatrix.
1197 : maechler 1758 * R/Rsparse.R (.R.2.C): R-level workaround since C-level
1198 :     R_to_CMatrix segfaults on one platform.
1199 : maechler 1760 Eliminate most coercion method to *specific* classes, and replace
1200 :     with virtual classes coercions.
1201 : maechler 1758
1202 : maechler 1760
1203 : maechler 1758 2007-02-01 Martin Maechler <maechler@stat.math.ethz.ch>
1204 :    
1205 :     * src/init.c: export the CHM...._validate() placeholders, since
1206 :     they *are* called.
1207 :    
1208 : maechler 1760 * tests/Class+Meth.R (classCanCoerce): and starting to test
1209 : maechler 1758 all as(<from>, <to>)
1210 :    
1211 : maechler 1751 2007-01-30 Martin Maechler <maechler@stat.math.ethz.ch>
1212 :    
1213 :     * R/Tsparse.R ([): more care when subsetting triangular Tsparse
1214 :     * tests/indexing.R: tested now
1215 :     * tests/indexing.Rout.save: updated
1216 :    
1217 :     * src/Csparse.c (Csparse_to_dense): use Rkind = -1 for PATTERN to
1218 :     * src/chm_common.c (chm_dense_to_SEXP): return "ngeMatrix" when
1219 :     appropriate.
1220 :    
1221 :     * NAMESPACE: export a trivial
1222 :     * R/Matrix.R: drop() Matrix-method
1223 :    
1224 :     * R/AllClass.R: moved all prototypes to virtual super classes.
1225 :    
1226 :     * R/Rsparse.R: many more coercions to have less exceptions in
1227 :     * tests/Class+Meth.R:
1228 :    
1229 :     * R/Ops.R (Compare): tweak for case with NA
1230 :     * tests/simpl.R: hence another 'FIXME' eliminated
1231 :    
1232 : maechler 1747 2007-01-29 Martin Maechler <maechler@stat.math.ethz.ch>
1233 :    
1234 : maechler 1748 * R/diagMatrix.R (solve): the obvious methods for diagonalMatrix
1235 :     objects.
1236 :    
1237 : maechler 1747 * tests/Class+Meth.R (tstMatrixClass): now testing diag(), nnzero(),
1238 :     and more of "!", "&", "|", all, any; coercions
1239 :    
1240 :     * R/Rsparse.R: many coercions (which enable quite a few other
1241 :     methods), thanks to enhancements in
1242 :     * src/dgCMatrix.c (R_to_CMatrix): new, and
1243 :     * src/dgCMatrix.c (compressed_to_TMatrix): now for (d,l,n) ,
1244 :     symmetric & triangular and ..RMatrix objects.
1245 :    
1246 :     * src/TMatrix_as.c (Matrix_T_as_DENSE,Matrix_T_as_GENERAL):
1247 :     renamed file from src/dsTMatrix.c;
1248 :     now dealing with symmetric and triangular Tsparse coercions, both
1249 :     to dense and general.
1250 :    
1251 :     2007-01-27 Martin Maechler <maechler@stat.math.ethz.ch>
1252 :    
1253 :     * src/dsTMatrix.c: has now "l" and "n" methods besides the "d" ones.
1254 :    
1255 :     * R/Ops.R (Arith): <dgCMatrix> o <numeric> now remains sparse
1256 :     where sensible when the <numeric> is of length > 1.
1257 :    
1258 :     2007-01-26 Martin Maechler <maechler@stat.math.ethz.ch>
1259 :    
1260 :     * R/Matrix.R ([<-): for M[] <- value: fix length
1261 :    
1262 :     2007-01-25 Martin Maechler <maechler@stat.math.ethz.ch>
1263 :    
1264 :     * R/Auxiliaries.R (n2l_Matrix): new, to be used in
1265 :     * R/ndenseMatrix.R: new coercions n* -> l*
1266 :    
1267 : maechler 1738 2007-01-22 Martin Maechler <maechler@stat.math.ethz.ch>
1268 :    
1269 :     * R/triangularMatrix.R: new file; simple triu() and tril() methods.
1270 :    
1271 :     * R/Ops.R ("Logic"): and other "Ops", many updates
1272 :    
1273 :     2007-01-18 Martin Maechler <maechler@stat.math.ethz.ch>
1274 :    
1275 :     * src/Mutils.h (SET_DimNames): new utility
1276 :    
1277 :     * R/Auxiliaries.R (nnzero): improved and now exported via
1278 :    
1279 :     * NAMESPACE: + nnzero(); length() == prod(dim(.)) method for all "Matrix" objects
1280 :    
1281 : maechler 1725 2007-01-17 Martin Maechler <maechler@stat.math.ethz.ch>
1282 :    
1283 :     * R/diagMatrix.R (!): fix typo.
1284 :    
1285 :     2007-01-16 Martin Maechler <maechler@stat.math.ethz.ch>
1286 :    
1287 :     * R/Auxiliaries.R (as_Csparse): and quite a few others:
1288 :     allow to pass class definition --> speedup
1289 :     * R/sparseMatrix.R: apply the above
1290 :    
1291 :     * R/Csparse.R: coercion Csparse* to dense* now preserves shape properties.
1292 :    
1293 :     * src/Mutils.h (mMatrix_as_geMatrix): new, based on
1294 :     * src/Mutils.c (dup_mMatrix_as_geMatrix): new; generalization of
1295 :     old dup_mMatrix_as_dgeMatrix), eliminating a long-standing "FIXME".
1296 :    
1297 :     * src/dense.c (dense_to_Csparse): use new mMatrix_as_geMatrix()
1298 :    
1299 :     * R/denseMatrix.R (.dense2C): based on dense_to_Csparse: name it,
1300 :     and use it for "sparse*" as well, since it's faster than the
1301 :     as_Csparse(.) way.
1302 :    
1303 :     2007-01-15 Martin Maechler <maechler@stat.math.ethz.ch>
1304 :    
1305 :     * R/Ops.R ("Logic"): more methods, notably an <lgC> o <lgC> one.
1306 :    
1307 : maechler 1724 2007-01-12 Martin Maechler <maechler@stat.math.ethz.ch>
1308 :    
1309 :     * R/Tsparse.R (.TM.repl.i.2col): new internal function to be used
1310 :     as method for M[ ij ] <- v
1311 :     * R/Csparse.R:: go via Tsparse for "M[ij] <- v"
1312 :    
1313 :     * R/Ops.R: "Compare" for (C|R)sparse: need pointer slot for all
1314 :     FALSE answer
1315 :    
1316 :     * R/Csparse.R (replCmat): fix the "all non-zero" case with reordering
1317 :     * tests/indexing.R: test it, and some of the above
1318 :    
1319 :     2007-01-05 Martin Maechler <maechler@stat.math.ethz.ch>
1320 :    
1321 :     * R/Auxiliaries.R (is_duplicatedT): new utility
1322 :    
1323 : bates 1716 2007-01-05 Douglas Bates <bates@stat.wisc.edu>
1324 :    
1325 :     * src/init.c (R_init_Matrix): export cholmod_scale
1326 :    
1327 : maechler 1724 2006-12-30 Martin Maechler <maechler@stat.math.ethz.ch>
1328 :    
1329 :     * R/zzz.R (tmp): for R >= 2.5.0, extend formals of our
1330 :     base::as.matrix to (x, ...)
1331 :    
1332 : maechler 1714 2006-12-28 Martin Maechler <maechler@stat.math.ethz.ch>
1333 :    
1334 :     * R/Ops.R ("Arith" etc): move almost all "Ops" methods to new R
1335 :     file; start using "Logic", hence
1336 :    
1337 :     * DESCRIPTION (Depends): R >= 2.4.1 (since we want "Logic")
1338 :     * NAMESPACE: import and export "Logic"
1339 :    
1340 :     2006-12-27 Martin Maechler <maechler@stat.math.ethz.ch>
1341 :    
1342 :     * src/zpotfr.f and dependencies: use LAPACK 3.1 version
1343 :     only needed previously to R version 2.5.0.
1344 : maechler 1724
1345 : maechler 1710 2006-12-26 Martin Maechler <maechler@stat.math.ethz.ch>
1346 :    
1347 :     * DESCRIPTION (Date, Version): 0.9975-8, ready for release
1348 :    
1349 :     * R/Tsparse.R (replTmat): fix subassignment of triangular
1350 :     * R/Csparse.R (replCmat): ditto
1351 :     * tests/indexing.R: more tests, incl the above fix
1352 :    
1353 :     2006-12-23 Martin Maechler <maechler@stat.math.ethz.ch>
1354 :    
1355 :     * R/Auxiliaries.R (drop0): extend for non CSparse
1356 :     * R/Auxiliaries.R (diagU2N): should work for all sparseMatrix
1357 :    
1358 :     * src/Csparse.c (Csparse_to_Tsparse, Csparse_general_to_symmetric):
1359 :     use uplo correctly (!); other places: use uplo_P() macro
1360 :    
1361 :     * R/Csparse.R (replCmat): call diagU2N() when needed
1362 :     * R/Tsparse.R (replTmat): ditto
1363 :    
1364 :     * src/dtCMatrix.c (tCMatrix_validate): new
1365 :     * src/dtTMatrix.c (tTMatrix_validate): new, used in
1366 :     * R/AllClass.R: for validity of dtC, dsC, and dtT, dsT.
1367 :    
1368 :     * R/diagMatrix.R (replDiag): to use in [<-
1369 :    
1370 : maechler 1708 2006-12-22 Martin Maechler <maechler@stat.math.ethz.ch>
1371 :    
1372 :     * R/Auxiliaries.R (as_Csparse2, as_geSimpl): new functions;
1373 :     also more general diagU2N().
1374 :    
1375 :     2006-12-21 Martin Maechler <maechler@stat.math.ethz.ch>
1376 :    
1377 :     * R/bind2.R: new file for all cbind2(), rbind() methods moved here
1378 :     from R/<foo>Matrix.R files. Better diagonal & improved sparse methods.
1379 :    
1380 : maechler 1707 2006-12-20 Martin Maechler <maechler@stat.math.ethz.ch>
1381 :    
1382 :     * tests/bind.R: a few more cases
1383 :     * R/Auxiliaries.R (.M.kind): also work for atomic vectors
1384 :    
1385 :     * R/denseMatrix.R (cbind2/rbind2): moved here (and generalized) from
1386 :     * R/ddenseMatrix.R (cbind2/rbind2)
1387 :     * R/Tsparse.R (replTmat): final(?!) fix for "[<-" ..
1388 :     * tests/indexing.R
1389 :     * tests/indexing.Rout.save: updated
1390 :    
1391 :     2006-12-18 Martin Maechler <maechler@stat.math.ethz.ch>
1392 :    
1393 :     * R/Tsparse.R (replTmat): fixed a remaining "[<-" bug in
1394 :     * tests/indexing.R
1395 :    
1396 : maechler 1705 2006-12-15 Martin Maechler <maechler@stat.math.ethz.ch>
1397 :    
1398 :     * R/sparseMatrix.R (prSpMatrix): "." alignment much improved:
1399 :     align with proper position of "0", i.e., right for integers.
1400 :     argument 'align' by default is "fancy".
1401 :    
1402 :     2006-12-14 Martin Maechler <maechler@stat.math.ethz.ch>
1403 :    
1404 :     * R/sparseMatrix.R: delegate "Compare" to "Csparse.."
1405 :     * R/Csparse.R: and fix "Compare" for more cases.
1406 :     * tests/Class+Meth.R: test some of these (m == m, m != m)
1407 :    
1408 :     2006-12-13 Martin Maechler <maechler@stat.math.ethz.ch>
1409 :    
1410 :     * R/lsparseMatrix.R: all() and any() methods
1411 :     * R/ldenseMatrix.R: ditto
1412 :     * NAMESPACE, R/Matrix.R: ditto
1413 :    
1414 :     * man/all-methods.Rd: document them minimally
1415 :    
1416 :     * tests/simple.R: add a few examples for these
1417 :    
1418 : maechler 1696 2006-12-11 Martin Maechler <maechler@stat.math.ethz.ch>
1419 :    
1420 :     * R/Tsparse.R ([): fix long standing typo in symmetric case
1421 :     * man/dsCMatrix-class.Rd: add example exhibiting the above case
1422 :    
1423 : bates 1691 2006-12-10 Douglas Bates <bates@stat.wisc.edu>
1424 :    
1425 :     * src/CHMfactor.c (CHMfactor_to_sparse): change LDL factorization
1426 :     to LL before converting to a sparse matrix. (The LDL form can be
1427 :     converted to a sparse matrix but it is implicitly a unit
1428 :     triangular matrix and a diagonal matrix overwritten on the diagonal.)
1429 :    
1430 :     2006-12-09 Douglas Bates <bates@stat.wisc.edu>
1431 :    
1432 :     * src/chm_common.c (chm_factor_to_SEXP): allocate and fill the Dim slot.
1433 :    
1434 : bates 1688 2006-12-08 Douglas Bates <bates@stat.wisc.edu>
1435 :    
1436 :     * DESCRIPTION (Version): updated -> release 0.9975-7
1437 :     * src/{init.c,chm_common.c}, inst/include/*: export cholmod_analyze_p
1438 :    
1439 : maechler 1682 2006-11-30 Martin Maechler <maechler@stat.math.ethz.ch>
1440 :    
1441 :     * R/diagMatrix.R (%*%): write a direct [diag o Csparse] method
1442 :    
1443 : bates 1681 2006-11-29 Douglas Bates <bates@stat.wisc.edu>
1444 :    
1445 :     * src/dgeMatrix.c (dgeMatrix_solve): Check error code from dgetri.
1446 :     * tests/dg_Matrix.R: Add Barry Rowlingson's test of a matrix that
1447 :     is exactly singular.
1448 :    
1449 : maechler 1674 2006-11-07 Martin Maechler <maechler@stat.math.ethz.ch>
1450 :    
1451 :     * DESCRIPTION (Date): updated -> release 0.9975-6
1452 :    
1453 : maechler 1673 2006-11-06 Martin Maechler <maechler@stat.math.ethz.ch>
1454 :    
1455 :     * R/Csparse.R (replCmat): symmetric indexing of symmetric matrix
1456 :     now returns symmetric.
1457 :    
1458 :     * R/zzz.R ("diag<-"): replace "diag<-" in base for R <= 2.4.x
1459 :    
1460 :     * R/Matrix.R (.M.sub.i.2col): new, for M[ cbind(i,j) ] indexing.
1461 :     * R/Matrix.R (.M.repl.i.2col): new, for M[ cbind(i,j) ] <- value
1462 :    
1463 :     * R/Auxiliaries.R (.type.kind): added
1464 :    
1465 :     2006-11-04 Martin Maechler <maechler@stat.math.ethz.ch>
1466 :    
1467 :     * src/cs.[ch]: updated to CSparse Version 2.0.3 by simply
1468 :     running src/CSparse_install.sh
1469 :    
1470 :     * R/denseMatrix.R: "[": keep symmetric on symmetric indexing.
1471 :    
1472 : maechler 1665 2006-11-03 Martin Maechler <maechler@stat.math.ethz.ch>
1473 :    
1474 :     * src/dsCMatrix.c (dsCMatrix_Csparse_solve): new
1475 :     * R/dsCMatrix.R (solve): "fully-sparse" using the above.
1476 :    
1477 :     * R/AllClass.R: "pMatrix" now also inherits from "generalMatrix"
1478 :    
1479 :     * tests/Class+Meth.R (tstMatrixClass): now assure
1480 :     the (important in method programming) property :
1481 :    
1482 :     ###>> Every "Matrix" is either
1483 :     ###>> "general*", "symmetric*", "triangular*" or "diagonal*"
1484 :    
1485 :     (where "*" stands for "Matrix")
1486 :    
1487 :     * R/Auxiliaries.R (diagU2N): now .Call()s Csparse_diagU2N for <Csparse>
1488 :    
1489 :     * R/dMatrix.R (Compare(<dMatrix>,<dMatrix>): update and
1490 :     * tests/validObj.R: checks for "comparison"
1491 :    
1492 :     * R/sparseMatrix.R ([): improved indexing for sparse;
1493 :     trying to keep <symmetric>[ n, n] symmmetric
1494 :    
1495 :     * tests/indexing.R: indexing for logical sparse now ok
1496 :    
1497 :    
1498 : maechler 1660 2006-11-02 Martin Maechler <maechler@stat.math.ethz.ch>
1499 :    
1500 : maechler 1661 * src/Tsparse.c: use xTsparse_validate() , and hence remove
1501 :    
1502 :     * src/{ltC,lsC,lgT}Matrix.[ch]: removed
1503 :    
1504 :     2006-11-02 Martin Maechler <maechler@stat.math.ethz.ch>
1505 :    
1506 : maechler 1660 * R/AllClass.R (Matrix-class): check length of dimnames in validity.
1507 :    
1508 :     * tests/simple.R: validObject() checking the above.
1509 :    
1510 : maechler 1665 * src/dgCMatrix.c (xCMatrix_validate): new, small and simple,
1511 : maechler 1660 replacing both dgCMatrix_validate and lgCM*.
1512 :    
1513 :     * src/Csparse.c (Csparse_dense_prod, etc): do not lose dimnames;
1514 :     fix dimnames setting in other places.
1515 :     * src/chm_common.c (chm_dense_to_SEXP): now can pass dimnames
1516 :    
1517 : maechler 1659 2006-11-01 Martin Maechler <maechler@stat.math.ethz.ch>
1518 :    
1519 : maechler 1660 * R/Csparse.R,src/Csparse.c, etc: tcrossprod(<CsparseM>,<CsparseM>)
1520 :    
1521 :     * R/sparseMatrix.R (isSymmetric): drop 'factors' slot for
1522 :     symmetry test, via
1523 : maechler 1659 * R/Auxiliaries.R (.as.dgC.0.factors):
1524 :    
1525 : bates 1657 2006-11-01 Douglas Bates <bates@r-project.org>
1526 :    
1527 :     * R/Csparse.R,src/Csparse.c,tests/matprod.R,
1528 :     man/CsparseMatrix-class.Rd: crossprod(<CsparseMatrix>,
1529 :     <CsparseMatrix>) added
1530 :    
1531 : maechler 1655 2006-10-30 Martin Maechler <maechler@stat.math.ethz.ch>
1532 :    
1533 :     * tests/matprod.R: add a variation of Harri's example
1534 :    
1535 :     * R/dsparseMatrix.R: fix crossprod(<dsparse>, <dge>) to *not*
1536 :     recursive infinitely.
1537 :    
1538 :     * R/dgCMatrix.R: + solve(<sparse>, <sparse>)
1539 :    
1540 :     * tests/indexing.R: add test for the "<" bug fixed 10-27 in R/dMatrix.R
1541 :    
1542 :     2006-10-28 Martin Maechler <maechler@stat.math.ethz.ch>
1543 :    
1544 :     * tests/Class+Meth.R (tstMatrixClass): more: use non-trivial
1545 :     matrix if possible; test m+m == 2*m; now test dgRMatrix.
1546 :     * R/dgRMatrix.R (.to.dgR): a few more coercions, in order to
1547 :     satisfy the above test.
1548 :    
1549 : maechler 1654 2006-10-27 Martin Maechler <maechler@stat.math.ethz.ch>
1550 :    
1551 : maechler 1655 * R/Matrix.R (Ops): <Matrix> o <matrix> method added
1552 :    
1553 : maechler 1654 * R/dgCMatrix.R: solve(a, b="missing") based on
1554 :     * src/dgCMatrix.c (dgCMatrix_matrix_solve): extend to work with
1555 :     RHS = NULL.
1556 :    
1557 :     * R/diagMatrix.R (diagdiagprod): extend %*% etc to ldiMatrix;
1558 :     add more (needed) [t]crossprod() methods.
1559 :    
1560 :     * man/ddiMatrix-class.Rd: more info, notably on 'diag'
1561 :    
1562 :     * R/Auxiliaries.R (as_CspClass): cleanup
1563 :     (drop0): internal utility for "Csparse_drop(*, 0)"
1564 :     (.bail.out.2): encourage active feedback
1565 :    
1566 :     2006-10-26 Martin Maechler <maechler@stat.math.ethz.ch>
1567 :    
1568 :     * R/dMatrix.R(Compare): new(), then slots [no validity check]
1569 :    
1570 :     * src/Csparse.c (Csparse_validate): fixed (and more efficient in
1571 :     non-valid or 'sorted' case).
1572 :    
1573 :     * R/dsparseMatrix.R: add "chol" method.
1574 :     * R/ddenseMatrix.R: ditto
1575 :    
1576 :     * R/diagMatrix.R (Ops): group methods for <diagonal> o <sparse>
1577 :     * NAMESPACE (Ops)
1578 :     * R/diagMatrix.R (diag2T): simple utility used "higher level"
1579 :     coercion; deprecating direct lower level coercions.
1580 :    
1581 :     * R/*.R (seq): use seq_len() and seq_along() where possible.
1582 :    
1583 :    
1584 : maechler 1647 2006-10-23 Martin Maechler <maechler@stat.math.ethz.ch>
1585 :    
1586 :     * DESCRIPTION (Version): 0.9975-5 ready for release
1587 :    
1588 : bates 1646 2006-10-20 Douglas Bates <bates@stat.wisc.edu>
1589 :    
1590 :     * src/init.c (R_init_Matrix): export more cholmod CCallable functions.
1591 :    
1592 : maechler 1642 2006-10-20 Martin Maechler <maechler@stat.math.ethz.ch>
1593 :    
1594 :     * R/AllClass.R (corMatrix): add 'validity' check;
1595 :     comment out unused "LDL" class definition
1596 :     * NAMESPACE: mention, but do not export "LDL" class
1597 :     * R/corMatrix.R: new (simple), needed for R-devel with
1598 :     * tests/Class+Meth.R (tstMatrixClass): 1 exception for corMatrix
1599 :     coerce and t() exceptions for all 5 'Mat.MatFact' classes.
1600 :    
1601 : bates 1641 2006-10-19 Douglas Bates <bates@stat.wisc.edu>
1602 :    
1603 :     * src/chm_common.h: Add R_cholmod_start to initialize cholmod to
1604 :     use Rprintf and R's error handling.
1605 :    
1606 : maechler 1635 2006-10-17 Martin Maechler <maechler@stat.math.ethz.ch>
1607 :    
1608 :     * R/diagMatrix.R (%*%): rep(*, each = .) in Matrix %*% diagonal.
1609 :     * tests/matprod.R: add tests for the bug fixed.
1610 :    
1611 : bates 1624 2006-10-11 Douglas Bates <bates@stat.wisc.edu>
1612 :    
1613 :     * src/HBMM.[ch]: remove HarwellBoeing format for writing.
1614 :     * src/SOURCES_C.mkf (SOURCES_C): no longer compile iohb.c
1615 :    
1616 :     2006-10-06 Douglas Bates <bates@stat.wisc.edu>
1617 :    
1618 : bates 1629 * R/d[gs]CMatrix.R: deprecate the writeHB function. Use writeMM instead.
1619 : bates 1624
1620 : maechler 1618 2006-10-06 Martin Maechler <maechler@stat.math.ethz.ch>
1621 :    
1622 :     * DESCRIPTION (Version): 0.9975-3
1623 :    
1624 :     * R/diagMatrix.R (bdiag): new function constructing block diagonal
1625 :     (sparse) matrices.
1626 :     * man/bdiag.Rd: docu + examples
1627 :    
1628 : maechler 1619 * R/Csparse.R (replCmat): calling new Csparse_drop() now.
1629 :    
1630 : maechler 1618 * src/Csparse.c (Csparse_general_to_symmetric, Csparse_drop): new functions
1631 :     * R/lsCMatrix.R: three more coercions to lsC (thanks to the above)
1632 :    
1633 :     * R/diagMatrix.R (Diagonal): '[<-' method for diag.matrices such
1634 :     that result is sparse or diagonal (and not dense).
1635 :    
1636 :     * man/Subassign-methods.Rd: fix examples
1637 :    
1638 :     * R/Matrix.R (Matrix): Matrix(0, *) or Matrix(*, sparse=TRUE)
1639 :     should always return a sparse (and not sometimes a diagonal) matrix.
1640 :    
1641 : maechler 1615 2006-10-05 Martin Maechler <maechler@stat.math.ethz.ch>
1642 :    
1643 :     * R/Matrix.R ([<-): also for value "Matrix" or "matrix"
1644 :    
1645 : bates 1613 2006-10-04 Douglas Bates <bates@stat.wisc.edu>
1646 :    
1647 :     * DESCRIPTION (Version): 0.9975-2
1648 : maechler 1615
1649 : bates 1613 * inst/include/Matrix_stubs.c (M_cholmod_sparse_to_triplet): export more symbols
1650 :    
1651 : bates 1611 2006-10-02 Douglas Bates <bates@R-project.org>
1652 :    
1653 :     * tests/dg_Matrix.R: Simplify test taking into account new code.
1654 :    
1655 : maechler 1599 2006-09-29 Martin Maechler <maechler@stat.math.ethz.ch>
1656 :    
1657 : maechler 1600 * R/Csparse.R (replCmat): improve for missing i / j in non-simple cases
1658 :    
1659 : maechler 1599 * R/lsTMatrix.R: new files w/ missing methods
1660 :     * R/nsTMatrix.R: " 'for completeness'
1661 :    
1662 :     * tests/Class+Meth.R: a bit less 'not.ok.classes'
1663 :    
1664 :     * R/Tsparse.R (t): generalized "t" method from "dgT*" to "Tsparse*"
1665 :    
1666 :    
1667 : bates 1595 2006-09-28 Douglas Bates <bates@R-project.org>
1668 :    
1669 :     * src/dppMatrix.h: Ensure definition of dspMatrix_validate is
1670 :     included.
1671 :    
1672 :     * src/init.c, inst/include/{Matrix.h,Matrix_stubs.h,cholmod.h}:
1673 :     Export C-callable functions used in Zt_create in lme4.
1674 :    
1675 : maechler 1592 2006-09-28 Martin Maechler <maechler@stat.math.ethz.ch>
1676 :    
1677 :     * DESCRIPTION (Version): 0.9975-1
1678 :    
1679 :     * tests/simple.R: less checks fail; using NA, found that our
1680 :     kronecker() is not base-compatible with NA's.
1681 :    
1682 :     * R/dMatrix.R: "Compare" method now implemented for all cases
1683 :    
1684 :     * R/Auxiliaries.R (indTri): == which([lower/upper].tri( * )) new utility
1685 :    
1686 :     * man/dtpMatrix-class.Rd: mention length of 'x' slot
1687 :    
1688 :     * src/dtpMatrix.c (dtpMatrix_validate): fix check
1689 :     * src/dspMatrix.c (dspMatrix_validate): ditto
1690 :    
1691 :     * R/dtTMatrix.R (gt2tT): fix ("l" -> "n")
1692 :     including coercion to [nl]tTMatrix.
1693 :    
1694 :     * R/diagMatrix.R (show): print a header line as for other classes.
1695 :    
1696 :     2006-09-27 Martin Maechler <maechler@stat.math.ethz.ch>
1697 :    
1698 :     * src/Makefile.win (SUBDIRS): fix typo
1699 :    
1700 : maechler 1583 2006-09-19 Martin Maechler <maechler@stat.math.ethz.ch>
1701 :    
1702 :     * DESCRIPTION (Date): ready to release 0.9975-0 to CRAN
1703 :    
1704 : bates 1577 2006-09-18 Douglas Bates <bates@stat.wisc.edu>
1705 :    
1706 :     * R/[CT]sparse.R (crossprod and tcrossprod): Handle the cases for x
1707 :     symmetric and y missing in R code using %*% (cholmod_aat doesn't
1708 :     accept a symmetric matrix).
1709 :     * tests/group-methods.R: Uncomment test of crossprod applied to
1710 :     lsCMatrix objects.
1711 :    
1712 : maechler 1575 2006-09-18 Martin Maechler <maechler@stat.math.ethz.ch>
1713 :    
1714 :     * R/AllClass.R (symmetricMatrix): add validity method (available
1715 :     in C for a long time). Many "n..Matrix": drop (wrong) validity arg.
1716 :    
1717 :     * src/lgCMatrix.c (lgCMatrix_validate): check 'x' slot (!)
1718 :    
1719 :     * tests/indexing.Rout.save:
1720 :     * tests/indexing.R: additions, mainly for 'lsparse'
1721 :    
1722 :     * R/diagMatrix.R (Diagonal) & coercion to lgTMatrix: fixes for NA
1723 :     case.
1724 :    
1725 :     * R/Auxiliaries.R (nz.NA): new utility now used in nnzero()
1726 :    
1727 : maechler 1571 2006-09-16 Martin Maechler <maechler@stat.math.ethz.ch>
1728 :    
1729 : maechler 1572 * R/sparseMatrix.R (prSpMatrix): print logical NAs "visibly"
1730 :     as 'N' (1-letter - Ok?)
1731 :    
1732 : maechler 1571 * tests/group-methods.R: add test for logical + NAs
1733 :    
1734 :     * R/dMatrix.R ("Compare"): fix to work with NA's
1735 :    
1736 :     * R/AllClass.R: "Cholesky" etc now inherit from MatrixFactorization.
1737 :    
1738 :     * src/lgCMatrix.c (ncsc_to_matrix): renamed from lcsc_to_matrix()
1739 :     which is implemented.
1740 :    
1741 : maechler 1565 2006-09-15 Martin Maechler <maechler@stat.math.ethz.ch>
1742 :    
1743 : maechler 1571 * src/chm_common.c: coerce logical <-> double instead of
1744 :     typecasting; needed for "l" matrix handling in cholmod.
1745 : maechler 1565
1746 : maechler 1571 * tests/other-pkgs.R (graph): small extension in "graph" checks.
1747 :    
1748 : maechler 1565 * R/sparseMatrix.R (graphNEL -> Tsparse): method for weight case.
1749 :     (Tsp2grNEL): other fixes needed
1750 :    
1751 : maechler 1548 2006-09-11 Martin Maechler <maechler@stat.math.ethz.ch>
1752 :    
1753 :     * R/AllClass.R ("nMatrix"): and subclasses for "nonzero pattern"
1754 :     Matrices, since "lMatrix", also "lsparseM" can have NA
1755 :     * R/ndenseMatrix.R, etc: new source files
1756 :     * man/nsparseMatrix-classes.Rd, etc: new help files
1757 :     * tests/: adaptions
1758 :     * src/chm_common.c (chm_dense_to_SEXP): and others:
1759 :     new 'Rkind' argument: "l*" and "d*" both use CHOLMOD_REAL
1760 : maechler 1582 * src/Csparse.c, etc: ditto
1761 : maechler 1548
1762 : bates 1546 2006-09-11 Douglas Bates <bates@R-project.org>
1763 :    
1764 :     * src/Mutils.[ch],init.c inst/include/*.h: Move the
1765 :     alloc_d**Matrix functions to the lme4 package.
1766 :    
1767 : bates 1543 2006-09-09 Douglas Bates <bates@R-project.org>
1768 :    
1769 :     * src/dsCMatrix.c (dsCMatrix_Cholesky): igoring LDL = FALSE now
1770 : maechler 1544 fixed
1771 : bates 1543
1772 : maechler 1544 2006-09-09 Martin Maechler <maechler@stat.math.ethz.ch>
1773 :    
1774 : maechler 1548 * R/lMatrix.R: new
1775 :    
1776 : maechler 1544 * R/sparseMatrix.R (Tsp2grNEL): do not yet use graph::foo()
1777 :    
1778 :     * R/dgeMatrix.R: do not define tcrossprod() methods for "matrix"
1779 : maechler 1582 * man/tcrossprod.Rd: ditto
1780 : maechler 1544
1781 : bates 1538 2006-09-08 Douglas Bates <bates@stat.wisc.edu>
1782 :    
1783 :     * inst/include/Matrix_stubs.c,Matrix.h: Add declarations and stubs
1784 :     for exported functions
1785 :     * src/Makefile, src/CHOLMOD/Lib/Makefile, src/Metis,CAMD,CCOLAMD:
1786 :     Remove partitioning algorithms for sparse matrix reordering. The
1787 :     copyright on the Metis code was problematic and the methods were
1788 :     rarely used.
1789 :     * src/triplet_to_col.[ch],MMHB.[ch]: Remove triplet_to_col. Such
1790 :     operations are now done entirely in CHOLMOD code.
1791 :    
1792 : bates 1517 2006-09-06 Douglas Bates <bates@R-project.org>
1793 :    
1794 :     * src/Mutils.h: Remove functions that are no longer used.
1795 :    
1796 : bates 1507 2006-09-04 Douglas Bates <bates@R-project.org>
1797 :    
1798 :     * src/dtCMatrix.c (dtCMatrix_validate): rename functions.
1799 :     * src/DEPS.mkf: update
1800 :    
1801 : maechler 1481 2006-09-02 Martin Maechler <maechler@stat.math.ethz.ch>
1802 :    
1803 :     * created branches/Matrix-for-R-2.3.x; on trunk: do
1804 :     * DESCRIPTION (Version): 0.9975-0
1805 :     (Depends): R (>= 2.4.0)
1806 :    
1807 : bates 1475 2006-09-01 Douglas Bates <bates@R-project.org>
1808 :    
1809 :     * R/sparseMatrix.R: Added direct method to CsparseMatrix from graphNEL
1810 :    
1811 : maechler 1472 2006-09-01 Martin Maechler <maechler@stat.math.ethz.ch>
1812 :    
1813 :     * R/sparseMatrix.R: add coercion from "ANY" to "sparseMatrix"
1814 :     * R/denseMatrix.R: add coercion from "ANY" to "denseMatrix"
1815 :    
1816 :     * R/Matrix.R ([): use nargs() to disambiguate M[i] and M[i,]
1817 :    
1818 :     2006-08-31 Martin Maechler <maechler@stat.math.ethz.ch>
1819 :    
1820 :     * R/sparseMatrix.R (Arith): moved Arith group method one-level up
1821 :     from "dsparse" to "sparse" and now go via "Csparse" instead of "dgC"
1822 : maechler 1582 * R/dsparseMatrix.R: ditto
1823 :     * R/Csparse.R: ditto
1824 : maechler 1472
1825 :     2006-08-31 Martin Maechler <maechler@stat.math.ethz.ch>
1826 :    
1827 :     * R/dMatrix.R (Compare): improve availability of "<", etc
1828 :     * R/Auxiliaries.R (asTuniq): new; also make use of R 2.4.x print(*,max)
1829 :    
1830 : maechler 1467 2006-08-30 Martin Maechler <maechler@stat.math.ethz.ch>
1831 :    
1832 :     * R/dgCMatrix.R: aargh: "Arith(<dgC>, numeric)" was wrong because
1833 :     of a 0-index which was used as 1-index (..hmm)
1834 :    
1835 :     * R/sparseMatrix.R (prSpMatrix): fix printing an all-0 sparse Matrix
1836 :    
1837 :     * R/Auxiliaries.R (all0, is0): for 0-testing in presence of NA's
1838 :     * R/Auxiliaries.R (isTriMat): use all0() for 0-testing.
1839 : maechler 1582 (.is.diagonal): ditto
1840 : maechler 1467
1841 :     * R/lgTMatrix.R: as("matrix", "lgTMatrix"): warn about NA's
1842 :    
1843 :     * R/Matrix.R (Matrix): also work for NA data
1844 :    
1845 : maechler 1455 2006-08-28 Martin Maechler <maechler@stat.math.ethz.ch>
1846 :    
1847 :     * R/Matrix.R (Matrix): + 'forceCheck' argument; dimnames setting
1848 :     in all cases.
1849 :    
1850 : bates 1453 2006-08-27 Douglas Bates <bates@R-project.org>
1851 :    
1852 :     * src/dense.[ch],init.c, R/ddenseMatrix.R, man/band.Rd
1853 :     (ddense_band): Added triu, tril and band for ddenseMatrix objects.
1854 :    
1855 : maechler 1447 2006-08-25 Martin Maechler <maechler@stat.math.ethz.ch>
1856 :    
1857 :     * src/Mutils.c (dup_mMatrix_as_dgeMatrix): added all subclasses of
1858 :     subclasses of "ddenseMatrix"
1859 :     * src/init.c et al: outcomment dtrM*_as_dge* and dsyM*_as_dge*_
1860 :     * R/ddenseMatrix.R et al: setAs("ddenseMatrix", "dgeMatrix", ..)
1861 :     instead of half dozen specialized ones.
1862 :    
1863 : bates 1445 2006-08-25 Douglas Bates <bates@R-project.org>
1864 :    
1865 :     * R/lmer.R (qqmath method): Bug fix provided by Emmanuel Tillard
1866 :     <tillard@cirad.fr> - ordering standard errors to match effects.
1867 :    
1868 : bates 1439 2006-08-24 Douglas Bates <bates@R-project.org>
1869 : bates 1431
1870 : bates 1439 * src/lsCMatrix.c (lsCMatrix_trans): Remove lsCMatrix_chol based
1871 :     on R_ldl.
1872 :     * R/lCholCMatrix.R,
1873 :     src/[dl]CholCMatrix.[ch],R_ldl.[ch],Metis_utils.[ch]: removed
1874 :     * src/dsCMatrix.c (dsCMatrix_to_dgTMatrix): use CHOLMOD
1875 :     * many files in ./R and ./src: Use more general version of
1876 :     dup_mMatrix_as_dgeMatrix to simplify method definitions.
1877 : bates 1442 * src/Mutils.c (dup_mMatrix_as_dgeMatrix): Add ddiMatrix,
1878 :     dtpMatrix, dspMatrix and dppMatrix conversions.
1879 :    
1880 : maechler 1447
1881 : bates 1439 2006-08-23 Douglas Bates <bates@R-project.org>
1882 :    
1883 :     * R/AllClass.R,lCholCMatrix.R,src/SOURCES_C.mkf,init.c,NAMESPACE:
1884 :     Remove classes lCholCMatrix and dCholCMatrix based on R_ldl code.
1885 : bates 1431 * src/dgeMatrix.c: Ensure 'factors' slot exists in result of
1886 :     dgeMatrix_crossprod (may need to do this in other places).
1887 :     * R/AllGeneric.R,dsCMatrix.R, src/dscMatrix.[ch]: Add Cholesky
1888 :     generic and method for dsCMatrix. Use CHOLMOD for chol().
1889 :    
1890 : bates 1414 2006-08-22 Douglas Bates <bates@R-project.org>
1891 :    
1892 :     * src/Mutils.c (dup_mMatrix_as_dgeMatrix): updated for general
1893 :     types of classed Matrices, matrices or numeric or logical vectors.
1894 : bates 1423 * src/init.c: register dup_mMatrix_as_dgeMatrix for coercions.
1895 :     * src/chm_common.c,Mutils.h (as_cholmod_factor): Move check_class
1896 :     to Mutils.h (as an inline) and change name to Matrix_check_class;
1897 :     fixes in as_cholmod_factor and chm_factor_to_SEXP.
1898 :     * src/dsCMatrix.[ch]: Use CHOLMOD for dsCMatrix_chol and
1899 :     dsCMatrix_matrix_solve. Comment out vestigial functions.
1900 :     * src/Csparse.c: use diag_P and uplo_P macros.
1901 : maechler 1447
1902 : bates 1405 2006-08-21 Douglas Bates <bates@R-project.org>
1903 :    
1904 :     * src/lmer.c (internal_mer_RZXinv): Fix memory leak caught by
1905 : maechler 1447 valgrind.
1906 : bates 1411 * tests/matprod.R: Add tests to verify that 'solve' and '%*%' are
1907 :     inverses.
1908 :     * src/sparseQR.c (sparseQR_validate): add new validation test, fix
1909 :     -Wall warnings.
1910 :     * src/dppMatrix.c,dtrMatrix.c,dgCMatrix.c,dgeMatrix.c,dspMatrix.c:
1911 :     Use dup_mMatrix_as_dgeMatrix.
1912 : maechler 1447
1913 : bates 1403 2006-08-20 Douglas Bates <bates@R-project.org>
1914 :    
1915 :     * src/sparseQR.c: Fix thinko in sparseQR_resid_fitted.
1916 :     * tests/sparseQR.R: Added
1917 :     * man/sparseQR-class.Rd: Document methods for qr.* generics
1918 :     * R/sparseQR.R: Return correct # of coefs; fix cut-and-paste errors
1919 :    
1920 : bates 1398 2006-08-19 Douglas Bates <bates@R-project.org>
1921 :    
1922 :     * NAMESPACE, R/sparseQR.R, src/init.c,sparseQR.[ch],SOURCES_C.mkf:
1923 :     Added methods for sparseQR for qr.qy, qr.qty, qr.coef, qr.resid
1924 :     and qr.fitted.
1925 :     * src/Mutils.[ch]: Added dup_mMatrix_as_dgeMatrix utility
1926 :     * src/dgCMatrix.c: Check for ordering before storing q in dgCMatrix_QR
1927 :    
1928 : maechler 1389 2006-08-18 Martin Maechler <maechler@stat.math.ethz.ch>
1929 :    
1930 :     * R/AllGeneric.R: add "qr" and "chol" generics; via 'trick' since
1931 :     the base version has no "..." argument.
1932 :    
1933 :     * R/sparseMatrix.R (prSpMatrix): fix the triangular unit diagonal case.
1934 :    
1935 :     * R/Matrix.R: define and
1936 :     * NAMESPACE: export as.numeric() and as.logical() methods.
1937 :     Let's hope these do not badly slow down something...
1938 :     Finally export the zapsmall() method.
1939 :    
1940 : bates 1388 2006-08-17 Douglas Bates <bates@R-project.org>
1941 :    
1942 :     * src/dgCMatrix.[ch] (dgCMatrix_matrix_solve), src/init.c,
1943 :     R/dgCMatrix.R: solve methods for dgCMatrix and dense RHS.
1944 :     * src/dtCMatrix.c :Remove code that is no longer used
1945 :     * R/dtCMatrix.R: Use C code for diagU2N in CsparseMatrix classes
1946 :    
1947 : bates 1370 2006-08-14 Douglas Bates <bates@R-project.org>
1948 :    
1949 : bates 1373 * src/Csparse.[ch],init.c (Csparse_to_logical): Added utilities
1950 :     Csparse_to_logical and Csparse_symmetric_to_general.
1951 :     * R/dgCMatrix.R,dsCMatrix.R,Csparse.R : Consolidate general
1952 : maechler 1389 coercion methods between CsparseMatrix and TsparseMatrix.
1953 : bates 1373
1954 :     2006-08-14 Douglas Bates <bates@R-project.org>
1955 :    
1956 : bates 1370 * R/dtCMatrix.R,dgCMatrix.R,Csparse.R src/init.c,dgCMatrix.[ch],
1957 :     Csparse.[ch],chm_common.c,dense.c : Use CHOLMOD code and methods
1958 :     for CsparseMatrix, TsparseMatrix, denseMatrix or matrix when
1959 :     possible.
1960 :    
1961 : bates 1368 2006-08-12 Douglas Bates <bates@R-project.org>
1962 :    
1963 :     * src/chm_common.[ch],Csparse.[ch],Tsparse.[ch],CHMfactor.c,dtTMatrix.c,
1964 :     dgTMatrix.c,dgCMatrix.c,dsCMatrix.c,dtTMatrix.c, R/dsTMatrix.R,
1965 :     Tsparse.R,Csparse.R,dgTMatrix.R,dsCMatrix.R,lsCMatrix.R:
1966 :     generalize conversions between TsparseMatrix, CsparseMatrix,
1967 :     denseMatrix and matrix. Preserve triangularity property and
1968 :     propagate Dimnames in the easy cases.
1969 :    
1970 : bates 1365 2006-08-10 Douglas Bates <bates@R-project.org>
1971 :    
1972 :     * src/lmer.c: adjust checks in glmer_init for S4SXP
1973 :     * tests/validObj.R: check of all(eq) should be all(eq@x) - worked
1974 :     before S4SXP but for the wrong reasons.
1975 :    
1976 : bates 1354 2006-08-08 Douglas Bates <bates@R-project.org>
1977 :    
1978 : bates 1360 * src/Csparse.c (Csparse_crossprod): tcrossprod result has stype = -1.
1979 :     Later modified to return the upper triangle only.
1980 :     * R/dgTMatrix.R: Remove vestigial crossprod and tcrossprod methods.
1981 : maechler 1389
1982 : bates 1352 2006-08-07 Douglas Bates <bates@R-project.org>
1983 :    
1984 :     * src/Csparse.c (Csparse_crossprod): Set stype on result to avoid
1985 :     R-level conversion to a sparse symmetric class.
1986 :     * R/Tsparse.R,R/Csparse.R (crossprod and tcrossprod methods):
1987 :     Remove conversion to sparse symmetric classes (now done in C code).
1988 :    
1989 : maechler 1349 2006-08-07 Martin Maechler <maechler@stat.math.ethz.ch>
1990 :    
1991 : maechler 1351 * R/dgCMatrix.R: disable old crossprod and tcrossprod methods
1992 :     * man/band.Rd: adapt the \dontshow{} unit test.
1993 :    
1994 :     2006-08-07 Martin Maechler <maechler@stat.math.ethz.ch>
1995 :    
1996 : maechler 1349 * DESCRIPTION (Version): 0.995-14 for CRAN
1997 :    
1998 :     * tests/other-pkgs.R: oops: library(Matrix) outside *if* !
1999 :    
2000 :     * R/sparseMatrix.R (Tsp2grNEL): fixed Tsparse -> graph coercion
2001 :     * tests/other-pkgs.R: more checks, sparseMatrix -> graph
2002 :    
2003 :     * R/Auxiliaries.R (as_Tsparse, as_Rsparse): new
2004 :     * R/Tsparse.R (tril, triu, band): methods
2005 : bates 1352 * R/dgRMatrix.R (tril, ...): ditto
2006 :     * man/band.Rd: ditto
2007 : maechler 1349
2008 :     2006-08-04 Martin Maechler <maechler@stat.math.ethz.ch>
2009 :    
2010 :     * R/Matrix.R (head, tail): directly use utils:::head.matrix
2011 :     to be up-to-date automatically.
2012 :    
2013 : maechler 1346 2006-08-03 Martin Maechler <maechler@stat.math.ethz.ch>
2014 :    
2015 :     * DESCRIPTION (Version): 0.995-13 to be released to CRAN
2016 :    
2017 :     * DESCRIPTION (Lazydata): no, instead of 'yes' because it fails for:
2018 :     * data/CAex.R, inst/external/CAex_slots.rda: replacing data/CAex.rda
2019 :     * data/KNex.R, inst/external/KNex_slots.rda: replacing data/KNex.rda
2020 :     such that the S4 objects are always created by the current version
2021 :     of R and 'Matrix' class definitions.
2022 :    
2023 : bates 1342 2006-08-01 Douglas Bates <bates@R-project.org>
2024 :    
2025 :     * R/lmer.R (LMEoptimize method), tests/lmer.R,
2026 : maechler 1346 inst/external/test3comp.rda: Added warnings for convergence on
2027 : bates 1342 boundary and test cases.
2028 :    
2029 :     * src/lmer.c (mer_postVar): Modified to return the variances that
2030 :     are marginal to the fixed effects, not conditional on them (which
2031 :     is what the bVar slot contents represent).
2032 :    
2033 : bates 1338 2006-07-31 Douglas Bates <bates@R-project.org>
2034 :    
2035 :     * NAMESPACE, src/lmer.c, R/lmer.R (hatTrace): Add the hatTrace
2036 :     function which calls the C function mer_hat_trace2.
2037 : maechler 1346
2038 : bates 1342 * man/ranef.Rd: Include description of "postVar" argument and
2039 :     producing a caterpillar plot.
2040 : bates 1338
2041 : maechler 1335 2006-07-31 Martin Maechler <maechler@stat.math.ethz.ch>
2042 :    
2043 :     * NAMESPACE: change "correlation" to "corMatrix"
2044 :     * R/AllClass.R: to avoid clash with S3 class in 'nlme'.
2045 : bates 1352 * R/dpoMatrix.R: ditto
2046 :     * R/lmer.R: ditto
2047 : maechler 1335
2048 : bates 1338 2006-07-28 Douglas Bates <bates@R-project.org>
2049 :    
2050 :     * src/lmer.c (internal_mer_RZXinv): Split the calculation of the
2051 :     RZXinv slot's contents into a separate internal function that can
2052 :     be used in mer_hat_trace.
2053 :    
2054 : maechler 1331 2006-07-22 Martin Maechler <maechler@stat.math.ethz.ch>
2055 :    
2056 :     * R/Matrix.R: Coercions "Matrix" -> (sparse|dense)Matrix
2057 :     via new smart
2058 :     * R/Auxiliaries.R (as_Csparse, as_dense, .M.shapse): new
2059 :     utility functions.
2060 :    
2061 :    
2062 : maechler 1330 2006-07-21 Martin Maechler <maechler@stat.math.ethz.ch>
2063 :    
2064 : maechler 1331 * R/Csparse.R (tril, triu, band): do return *triangular* classed
2065 :     matrices when appropriate; band() even symmetric ones.
2066 :     (replCmat): extend to potentially all "CsparseMatrix"
2067 :     * R/Tsparse.R (replTmat): extend to all "TsparseMatrix"; hence
2068 :     allow subassignment for special sparse matrices.
2069 :    
2070 :     * R/Auxiliaries.R (as_geClass): factor out the .M.kind() functionality
2071 :    
2072 : maechler 1330 * src/lmer.c (mer_MCMCsamp, glmer_MCMCsamp): new 'verbose'
2073 :     argument; in glmer_*(): print only if(verbose).
2074 :    
2075 :     speed-optimize a few places by moving REAL(.) out of loops.
2076 :    
2077 :     * src/lmer.h, src/init.h, R/lmer.R: related to above.
2078 :    
2079 : maechler 1329 2006-07-20 Martin Maechler <maechler@stat.math.ethz.ch>
2080 :    
2081 :     * R/Matrix.R("["): disable ("Matrix", i = "logical", j = "missing"),
2082 :     since that wrongly triggers also for M[ logi , ]
2083 :    
2084 :     * R/denseMatrix.R: "[" methods now also work e.g. when indexing
2085 :     a symmetric matrix that results in a non-symmetric one.
2086 :     * R/Auxiliaries.R (as_geClass): new function used in "[" above.
2087 :    
2088 :     * R/dMatrix.R: make round(M) work as round(M, 0)
2089 :    
2090 :     * R/dgTMatrix.R (image): coordinate system and axis now use
2091 :     1-based indices, not 0-based ones.
2092 :    
2093 :     * R/Tsparse.R (.ind.prep for "["): get rid of max(<empty>) warning.
2094 :     * tests/indexing.R: test it.
2095 :    
2096 :     * NAMESPACE: export isSymmetric(); has been a generic in "base" for a while;
2097 :     * man/isSymmetric-methods.Rd: and document it.
2098 :    
2099 :     * R/SparseM-conv.R: added coercion methods for some 'SparseM' matrices.
2100 :     * man/SparseM-conv.Rd: docu them
2101 :    
2102 :     * tests/other-pkgs.R: renamed from tests/graph.R and add example
2103 :     for 'SparseM' conversions
2104 :    
2105 :     2006-07-17 Douglas Bates <Douglas.Bates@R-project.org>
2106 :    
2107 :     * R/Matrix.R (head): added head() and tail() methods.
2108 :    
2109 :     2006-07-17 Martin Maechler <maechler@stat.math.ethz.ch>
2110 :    
2111 :     * DESCRIPTION (Version): 0.995-12 released to CRAN
2112 :    
2113 : maechler 1319 2006-07-15 Martin Maechler <maechler@stat.math.ethz.ch>
2114 :    
2115 :     * tests/simple.R: add check for correct dsT -> dgT coercion;
2116 :     add check for correct printing of symmetric sparse matrices.
2117 :    
2118 :     * R/Auxiliaries.R (non0ind): return *all* non-0 entry indices also
2119 :     for sparse symmetric matrices.
2120 :    
2121 :     * src/dsTMatrix.c (dsTMatrix_as_dgTMatrix): do not copy the
2122 :     diagonal twice.
2123 :    
2124 : bates 1316 2006-07-11 Douglas Bates <Douglas.Bates@R-project.org>
2125 :    
2126 :     * src/dsTMatrix.c (dsTMatrix_as_dgTMatrix): Fix a case of INTEGER
2127 : maechler 1319 being applied to the x slot (detected by Brian Ripley).
2128 : bates 1316
2129 : maechler 1315 2006-07-10 Martin Maechler <maechler@stat.math.ethz.ch>
2130 :    
2131 :     * src/dgCMatrix.c (dgCMatrix_validate): 'p' slot must have correct length.
2132 :    
2133 :     * R/Auxiliaries.R (isTriC): fix buglet (we were 1-based!)
2134 :    
2135 :     2006-07-08 Martin Maechler <maechler@stat.math.ethz.ch>
2136 :    
2137 :     * src/lgCMatrix.c (lgCMatrix_diag): new function
2138 :     * R/lgCMatrix.R (diag): for new method
2139 :    
2140 :     * R/AllClass.R (TsparseMatrix): do use Tsparse_validate
2141 :     ==> construction of illegal "*gTMatrix" via new() should
2142 :     now be much less easy:
2143 :     * tests/Class+Meth.R: assertError() for some illegal "dgT*"
2144 :    
2145 :     * R/Matrix.R (Matrix): Matrix(0, nrow,ncol) now "goes sparse"
2146 :     directly.
2147 :     * man/Matrix.Rd: documents it.
2148 :    
2149 : bates 1311 2006-07-06 Douglas Bates <bates@R-project.org>
2150 :    
2151 :     * src/pedigree.c (pedigree_inbreeding): Correction in
2152 :     initialization. This function is not currently being used and is
2153 :     not fully tested.
2154 :    
2155 : bates 1312 * NAMESPACE, R/{AllClass.R,lmer.R}, src/{init.c,lmer.c}:
2156 :     Introduced the glmer class. Added code for mcmcmsamp on glmer
2157 :     objects. Modified validity check on pedigree objects to account
2158 :     for nonparallel patterns of missingness of parents.
2159 : bates 1311
2160 : bates 1313 * man/{lmer-class.Rd,mcmcsamp.Rd}: Update documentation for glmer
2161 :     class.
2162 : maechler 1315
2163 :     2006-07-01 Martin Maechler <maechler@stat.math.ethz.ch>
2164 :    
2165 :     * R/pMatrix.R: coercion pMatrix -> Tsparse
2166 :    
2167 : bates 1300 2006-06-12 Douglas Bates <bates@R-project.org>
2168 :    
2169 : maechler 1319 * DESCRIPTION (Version): 0.995-11 released to CRAN
2170 :    
2171 : bates 1300 * R/lmer.R (mcmcsamp method): Corrected arrangments of names on
2172 :     the output from mcmcsamp.
2173 :    
2174 : bates 1298 2006-06-10 Douglas Bates <bates@R-project.org>
2175 :    
2176 : bates 1300 * R/lmer.R (simulestimate): added C code for calculating the trace
2177 :     of the hat matrix.
2178 : bates 1298
2179 : maechler 1295 2006-06-09 Martin Maechler <maechler@stat.math.ethz.ch>
2180 :    
2181 :     * R/diagMatrix.R (setAs): define coercion methods to sparse matrix
2182 :     classes.
2183 : maechler 1315 * R/sparseMatrix.R etc: multiplication of diagonal and sparse
2184 : maechler 1295
2185 : maechler 1290 2006-06-08 Martin Maechler <maechler@stat.math.ethz.ch>
2186 :    
2187 :     * R/dgTMatrix.R (colSums): etc. All four of
2188 :     colSums(), rowSums(), colMeans(), rowMeans() now should work for
2189 :     all "Matrices".
2190 :    
2191 : bates 1288 2006-06-01 Douglas Bates <bates@stat.wisc.edu>
2192 :    
2193 :     * R/lmer.R (panel.ci): Add a reference line at zero and a
2194 :     background grid to the qqmath plot of ranef.lmer.
2195 :    
2196 : bates 1287 2006-05-30 Douglas Bates <bates@stat.wisc.edu>
2197 : bates 1284
2198 : bates 1287 * R/lmer.R (expandSlash): Functions (non-exported) to allow nested
2199 :     grouping factors to be specified in the formula as (1|foo/bar).
2200 :    
2201 :     2006-05-27 Douglas Bates <bates@stat.wisc.edu>
2202 :    
2203 : bates 1284 * R/lmer.R (findbars and others): Change check of is.numeric to
2204 :     !is.language to resolve the bug reported by Jacob Wegelin.
2205 :    
2206 :     * src/pedigree.c (pedigree_inbreeding): Initial implementation of
2207 :     code to evaluate inbreeding coefficients without calculating T,
2208 :     based on code in Sargolzaei and Iwaisaki's paper.
2209 :    
2210 : bates 1283 2006-05-27 Douglas Bates <bates@stat.wisc.edu>
2211 :    
2212 :     * R/{lmer.R,AllGeneric.R}, src/{init.c,lmer.[ch]}: Added local
2213 :     generic and mer methods for isNested and denomDF. This denomDF was
2214 :     an attempt to emulate that in lme but I don't think that makes
2215 :     sense. Use the trace of the hat matrix instead.
2216 :    
2217 : maechler 1271 2006-05-17 Martin Maechler <maechler@stat.math.ethz.ch>
2218 :    
2219 :     * R/sparseMatrix.R: Matrix <-> graph methods: can no longer use
2220 :     the C code depending on a slot structure that's no longer valid.
2221 : bates 1352 * src/dgTMatrix.c: ditto (also: src/init.c src/dgTMatrix.h)
2222 : maechler 1271
2223 :    
2224 : bates 1268 2006-05-17 Douglas Bates <bates@stat.wisc.edu>
2225 :    
2226 :     * R/{AllGeneric.R,Csparse.R},man/band.Rd,NAMESPACE: changed name
2227 :     of lowerTriMatrix generic and methods to tril (also upper to triu)
2228 :     and added a general band extractor.
2229 :    
2230 : bates 1267 2006-05-16 Douglas Bates <bates@stat.wisc.edu>
2231 :    
2232 :     * R/pedigree.R (pedigree): Replace sire and dam values outside the
2233 :     allowable range with NAs. Added a corresponding check in the
2234 :     validity check for the pedigree class.
2235 :    
2236 :     * R/[CT]sparse.R ([t]crossprod): The result of single-argument
2237 :     crossprod methods now inherits from symmetricMatrix.
2238 :    
2239 : bates 1265 2006-05-15 Douglas Bates <bates@stat.wisc.edu>
2240 :    
2241 :     * R/AllGeneric.R (lowerTriMatrix): Added (but did not export)
2242 :     generics lowerTriMatrix and upperTriMatrix along with methods for
2243 :     the Csparse virtual class. Also added a C function Csparse_band
2244 :     that implements these methods by calling cholmod_band.
2245 :    
2246 : maechler 1264 2006-05-15 Martin Maechler <maechler@stat.math.ethz.ch>
2247 :    
2248 :     * R/Tsparse.R ("["): column or row subsetting; @Dimnames[k] got
2249 :     erased when it was NULL. This led to invalid subselections!
2250 :    
2251 : bates 1259 2006-04-25 Douglas Bates <bates@stat.wisc.edu>
2252 :    
2253 :     * R/dtCMatrix.R: avoid coercion of dtCMatrix object to dgCMatrix
2254 :     in method for "t" so as not to lose the unit diagonal property.
2255 :    
2256 : bates 1257 2006-04-19 Douglas Bates <bates@stat.wisc.edu>
2257 :    
2258 :     * R/lmer.R, R/AllGeneric.R, NAMESPACE: Remove the postVar generic
2259 :     and methods. This is now an option to the ranef method for the
2260 :     mer class.
2261 :    
2262 :     * src/cs_utils.c: Ensure that the nz component is -1 for a
2263 :     compressed column-oriented matrix. Minor formatting cleanup.
2264 :    
2265 :     * man/lmer-class.Rd: Document the qqmath method for ranef.lmer
2266 :     objects.
2267 :    
2268 : maechler 1253 2006-04-19 Martin Maechler <maechler@stat.math.ethz.ch>
2269 :    
2270 :     * R/Auxiliaries.R (diagU2N): new for the solve() methods in
2271 :     * R/dtCMatrix.R: where dgC -> dgT coercion now preserves diag = "U".
2272 :    
2273 : bates 1251 2006-04-15 Douglas Bates <bates@stat.wisc.edu>
2274 :    
2275 :     * src/cs.[ch],src/cs_utils.[ch] : Added Tim Davis' CSparse library
2276 :     in cs.[ch] and utilities to interface to that code in cs_utils.[ch].
2277 :    
2278 :     * R/dtCMatrix.R, src/dtCMatrix.[ch] : CSparse-based solve methods
2279 :     for the dtCMatrix class.
2280 : maechler 1253
2281 : bates 1247 2006-04-12 Douglas Bates <bates@stat.wisc.edu>
2282 :    
2283 :     * R/pedigree.R, R/AllClass.R, NAMESPACE: added a pedigree class
2284 :     and methods for it.
2285 :    
2286 : maechler 1245 2006-04-12 Martin Maechler <maechler@stat.math.ethz.ch>
2287 :    
2288 :     * R/dgCMatrix.R: add storage.mode(.) <- "double" for "matrix"
2289 :     arguments, such that M %*% 1:6 now works
2290 :     * Tests/matprod.R: test the above
2291 :    
2292 : bates 1244 2006-04-03 Douglas Bates <bates@stat.wisc.edu>
2293 : bates 1243
2294 :     * R/lmer.R (qqmath,ranef.lmer-method): added a qqmath method for
2295 :     the ranef.lmer class.
2296 :    
2297 :     * R/AllClass.R, NAMESPACE, R/lmer.R: Added a postVar generic and
2298 :     methods to extract the posterior variances from the bVar slot.
2299 :    
2300 : maechler 1238 2006-03-30 Martin Maechler <maechler@stat.math.ethz.ch>
2301 :    
2302 :     * R/dtCMatrix.R: allow coercion from dgC* to triangular (dtC*)
2303 :     * R/dsCMatrix.R: and symmetric (dsC*) 'Csparse' matrices.
2304 :    
2305 :     * R/Tsparse.R: Tsparse* -> Csparse* coercion now works and is tested in
2306 :     * tests/simple: (extended)
2307 :    
2308 :     * R/sparseMatrix.R (isTriangular): now using much improved
2309 :     * R/Auxiliaries.R (isTriC): new triangularity check for *CMatrix
2310 :    
2311 : bates 1236 2006-03-23 Douglas Bates <bates@stat.wisc.edu>
2312 :    
2313 :     * src/dsyMatrix.c (dsyMatrix_as_dspMatrix): Propagate DimNames
2314 :     (problem report from Franklin Parlamis). This should be done
2315 : maechler 1238 generally.
2316 : bates 1236
2317 : bates 1234 2006-03-21 Douglas Bates <bates@stat.wisc.edu>
2318 :    
2319 :     * R/AllClass.R,lmer.R: Change the name of the lmer.ranef class to
2320 :     ranef.lmer (like summary.lmer). Add the coef.lmer class and
2321 :     update the plot methods.
2322 :    
2323 : bates 1232 2006-03-20 Douglas Bates <bates@stat.wisc.edu>
2324 :    
2325 :     * R/lmer.R (resid and ranef methods): Added methods for the
2326 :     "residuals" and "resid" generic but only for linear mixed model
2327 :     fits. Changed the ranef method to return a list of data frames so
2328 :     that the plot methods now work.
2329 :    
2330 : bates 1230 2006-03-16 Douglas Bates <bates@bates2>
2331 :    
2332 :     * src/dpoMatrix.c (dpoMatrix_chol): Require n > 0 in call to
2333 :     dpotrf - otherwise the BLAS on Mac OS X complains and quits.
2334 :    
2335 :     * DESCRIPTION (Date): New release
2336 :    
2337 : maechler 1228 2006-03-15 Martin Maechler <maechler@stat.math.ethz.ch>
2338 :    
2339 :     * DESCRIPTION (Version): 0.995-6 -- to be released to CRAN
2340 :    
2341 :     * data/KNex.rda: replacing 'mm' and 'y' by KNex <- list(mm=mm, y=y)
2342 :     * man/KNex.Rd: and other help files
2343 :     * tests/*.R: several ones needed adaption
2344 : bates 1352 * inst/doc/Comparisons.Rnw: ditto
2345 : maechler 1228
2346 : maechler 1226 2006-03-11 Martin Maechler <maechler@stat.math.ethz.ch>
2347 :    
2348 :     * R/dgCMatrix.R (replCmat): "[<-" methods for dgCMatrix
2349 :    
2350 :     * tests/indexing.R: tests for new [<- methods for sparse matrices.
2351 :    
2352 :     2006-03-10 Martin Maechler <maechler@stat.math.ethz.ch>
2353 :    
2354 :     * R/dgTMatrix.R (replTmat): "[<-" methods for dgTMatrix
2355 :    
2356 :     * R/Tsparse.R (.ind.prep): fix out-of-range indexing
2357 :    
2358 :     2006-03-08 Martin Maechler <maechler@stat.math.ethz.ch>
2359 :    
2360 :     * R/dMatrix.R: enable things like M [ M < 10 ]
2361 :     * R/dgeMatrix.R: implement it
2362 :    
2363 : maechler 1222 2006-03-06 Martin Maechler <maechler@stat.math.ethz.ch>
2364 :    
2365 :     * R/AllClass.R: define "summary.mer" and "*.lmer"
2366 :     * R/lmer.R (summary): summary(<mer>) computes & returns the above;
2367 :     * R/lmer.R (show): now works with summary()
2368 :    
2369 :     2006-03-04 Martin Maechler <maechler@stat.math.ethz.ch>
2370 :    
2371 :     * R/dgCMatrix.R: finally direct "Arith" dgC o dgC
2372 :     * R/Auxiliaries.R (WhichintersectInd): and other utilities to
2373 :     support the above
2374 :    
2375 : bates 1213 2006-02-07 Douglas Bates <bates@stat.wisc.edu>
2376 :    
2377 :     * R/lmer.R (lmer): fix initial values of offset and weights for glm.fit.
2378 :     Use glmFit$prior.weights for weights in a glmm.
2379 :     Allow an option usePQL = FALSE to skip the PQL steps for the
2380 :     Laplace method (and, in time, the AGQ method).
2381 :    
2382 :     * src/lmer.c (mer_factor): Move downdating and factoring of XtX
2383 :     into a separate function internal_mer_Xfactor to be able to call
2384 :     it from internal_bhat.
2385 :    
2386 : maechler 1200 2006-01-23 Martin Maechler <maechler@stat.math.ethz.ch>
2387 :    
2388 :     * tests/Class+Meth.R (tstMatrixClass): function for much better
2389 :     testing; now again of all actual classes.
2390 :    
2391 :     * src/Mutils.c (MAKE_TRIANGULAR_BODY, MAKE_SYMMETRIC_BODY):
2392 :     use macros and define make_d_matrix_* and make_i_matrix_*
2393 :     where _i_ is for the ldense routines:
2394 :    
2395 :     * src/ldense.c (ltrMatrix_as_lgeMatrix): provide functions
2396 :     * src/ldense.c (lsyMatrix_as_lgeMatrix):
2397 :    
2398 :     * R/ldenseMatrix.R: use the above in setAs(*,"lgeMatrix")
2399 :    
2400 :    
2401 : maechler 1174 2006-01-16 Martin Maechler <maechler@stat.math.ethz.ch>
2402 :    
2403 :     * R/Matrix.R (Matrix): has become much "smarter" now auto-producing
2404 :     many different kinds of matrices.
2405 :     * R/*.R: quite a few new methods were needed for R CMD check with
2406 :     new Matrix(). Very good for users playing around.
2407 :    
2408 :    
2409 : maechler 1165 2006-01-15 Martin Maechler <maechler@stat.math.ethz.ch>
2410 :    
2411 :     * src/dgeMatrix.c (dMatrix_validate): new
2412 :     * src/Mutils.c (dense_nonpacked_validate): new
2413 :    
2414 :     * src/dtrMatrix.c (dtrMatrix_validate): improved/fixed
2415 :    
2416 :    
2417 :     2006-01-14 Douglas Bates <bates@stat.wisc.edu>
2418 :    
2419 :     * R/AllClass.R (compMatrix), (generalMatrix): new virtual classes
2420 :    
2421 : bates 1123 2006-01-07 Douglas Bates <bates@stat.wisc.edu>
2422 : bates 1119
2423 : maechler 1127 * DESCRIPTION (Version): 0.99-6 released to CRAN
2424 :    
2425 : bates 1119 * src/dgBCMatrix.c (cscb_trcbsm): Fix due to Peter Dalgaard for
2426 :     segfault in cases with multiple non-nested grouping factors.
2427 :    
2428 : maechler 1109 2006-01-03 Martin Maechler <maechler@stat.math.ethz.ch>
2429 :    
2430 :     * DESCRIPTION (Version): 0.99-4 to be released to CRAN
2431 :     (Depends): also on 'utils'
2432 :    
2433 :     * R/AllClass.R (diagonalMatrix): new class with "ddi*" and "ldi*"
2434 :     * R/diagMatrix.R (Diagonal): constructor and methods for
2435 :     diagonal matrices
2436 :    
2437 :     * R/ltTMatrix.R: new "minimal methods"
2438 :    
2439 : maechler 1091 2005-12-12 Martin Maechler <maechler@stat.math.ethz.ch>
2440 :    
2441 :     * R/AllGeneric.R (tcrossprod): 2-argument version; here, and for
2442 :     all methods (and help files).
2443 :    
2444 : maechler 1084 2005-12-09 Martin Maechler <maechler@stat.math.ethz.ch>
2445 :    
2446 :     * R/Auxiliaries.R (dimNamesCheck): fixed thinko -> bug
2447 :     for case (dimn. op no_dimn.)
2448 :    
2449 :     2005-11-14 Douglas Bates <bates@stat.wisc.edu>
2450 :    
2451 : maechler 1174 * DESCRIPTION (Version): 0.99-2 released to CRAN
2452 : maechler 1084
2453 : bates 988 2005-10-21 Douglas Bates <bates@stat.wisc.edu>
2454 :    
2455 :     * R/lmer.R (simulate method): Fixed a drop=FALSE problem reported
2456 :     by Julian Faraway.
2457 :    
2458 : maechler 976 2005-10-06 Martin Maechler <maechler@stat.math.ethz.ch>
2459 :    
2460 :     * R/Auxiliaries.R (try_as): new utility
2461 :     * R/sparseMatrix.R: use try_as() in coercion to original class
2462 :    
2463 : maechler 956 2005-09-30 Martin Maechler <maechler@stat.math.ethz.ch>
2464 :    
2465 :     * src/dgCMatrix.c (double_to_csc): and dgeMatrix_to_csc()
2466 :    
2467 :     2005-09-29 Martin Maechler <maechler@stat.math.ethz.ch>
2468 :    
2469 :     * R/Auxiliaries.R (dimNamesCheck): added
2470 :    
2471 :     * R/Matrix.R (as.array), (as.vector): new
2472 :    
2473 : maechler 954 2005-09-28 Martin Maechler <maechler@stat.math.ethz.ch>
2474 :    
2475 :     * R/Matrix.R (Matrix): get logical argument 'sparse' with a smart
2476 : maechler 956 default.
2477 :     * R/AllClass.R: move 'factors' slot toplevel "Matrix";
2478 :     "pMatrix" now contains "sparseMatrix"
2479 : maechler 954
2480 : maechler 948 2005-09-26 Martin Maechler <maechler@stat.math.ethz.ch>
2481 :    
2482 :     * tests/Class+Meth.R: new tests; t(t(m)) == m
2483 :    
2484 :     * src/dtCMatrix.c (tsc_transpose): add forgotten "diag" slot
2485 :    
2486 :     * src/dsTMatrix.c (dsTMatrix_as_dsCMatrix): bad typo (segfault!)
2487 :     * src/dtTMatrix.c (dtTMatrix_as_dtCMatrix): new
2488 :    
2489 :     * R/dspMatrix.R: typo in "t" method
2490 :    
2491 : maechler 925 2005-09-18 Douglas Bates <bates@wisc.edu>
2492 :    
2493 :     * R/AllClass.R (TsparseMatrix), CsparseM* and RsparseM*
2494 :     * R/Tsparse.R: instead of R/gTMatrix.R
2495 :     * R/Csparse.R: new
2496 :     * src/Tsparse.c (Tsparse_to_Csparse): new; -> cholmod_()
2497 :     * src/Tsparse.c: new; many trivial methods calling cholmod_()
2498 :     * src/Csparse.c (Csparse_to_Tsparse), transpose, (mat|cross)prod:
2499 :     via cholmod
2500 :    
2501 :     2005-09-16 Martin Maechler <maechler@stat.math.ethz.ch>
2502 :    
2503 :     * R/Auxiliaries.R (non0ind): new function using new C code
2504 :     * src/dgCMatrix.c (compressed_non_0_ij): new utility
2505 :    
2506 : bates 917 2005-09-15 Douglas Bates <bates@localhost.localdomain>
2507 :    
2508 :     * src/chm_common.h: header file required by all C sources that
2509 : maechler 1174 call CHOLMOD functions. It defines a cholmod_common structure
2510 : bates 917 called 'c' whose address is passed as the last argument to
2511 :     (virtually) every CHOLMOD function.
2512 :    
2513 :     * src/Pattern.c: Simple example of the use of CHOLMOD.
2514 :    
2515 :     * src/init.c: initialize and finalize the cholmod_common structure.
2516 :    
2517 :     * src/Makefile: Added source packages CHOLMOD UMFPACK AMD COLAMD
2518 :     LDL and CCOLAMD from the U. of Florida sparse matrix library.
2519 :    
2520 : maechler 908 2005-09-08 Martin Maechler <maechler@stat.math.ethz.ch>
2521 :    
2522 :     * inst/test-tools.R: new file collecting the utility functions used
2523 :     in ./tests/*.R
2524 :    
2525 :     * R/ddenseMatrix.R (cbind2): new methods for "numeric" and "matrix"
2526 :     * R/Matrix.R (cbind2): methods for NULL and missing
2527 :    
2528 : maechler 886 2005-08-31 Martin Maechler <maechler@stat.math.ethz.ch>
2529 :    
2530 :     * R/AllClass.R: new "index" class for "[" and "[<-":
2531 :     First cut at "symmetricMatrix" and "triangularMatrix"
2532 :     * R/gTMatrix.R (.ind.prep): new function;
2533 : maechler 1174 Logical and character indexing now work too.
2534 : maechler 886 * R/Matrix.R: cheap "[<-" methods for denseMatrix now work
2535 :     * tests/indexing.R: new, including *.Rout.save
2536 :     * tests/dgTMatrix.R: new
2537 :    
2538 : bates 876 2005-08-29 Douglas Bates <bates@wisc.edu>
2539 :    
2540 :     * src/dgTMatrix.c (graphNEL_as_dgTMatrix): Corrected the position
2541 :     indicator pos not being updated. Also enforced upper triangular
2542 :     for symmetric case. Need to coerce edges component of elements of
2543 :     edge list - grr! (Why don't they define their classes cleanly?)
2544 :    
2545 : maechler 871 2005-08-26 Martin Maechler <maechler@stat.math.ethz.ch>
2546 :    
2547 :     * R/Matrix.R: added first "[<-" methods; not yet functional
2548 : bates 1352 * R/denseMatrix.R: ditto
2549 : maechler 871 * man/Subassign-methods.Rd: new help file for these
2550 :    
2551 :     2005-08-25 Martin Maechler <maechler@stat.math.ethz.ch>
2552 :    
2553 :     * DESCRIPTION (Version): 0.98-6
2554 :    
2555 :     * R/denseMatrix.R: new file for "[" fallback methods for all dense
2556 :     matrices.
2557 :    
2558 : maechler 868 2005-08-19 Martin Maechler <maechler@stat.math.ethz.ch>
2559 :    
2560 :     * src/lgCMatrix.c (lcsc_to_matrix): new; need for
2561 :     as( <logical>, "matrix")
2562 :    
2563 :     * R/pMatrix.R: coercion to "lgTMatrix"
2564 :    
2565 :     * R/gTMatrix.R: new virtual class to define "[" methods for.
2566 :     * man/gTMatrix-class.Rd:
2567 :     * General slight re-organization of where "[" methods are defined.
2568 :     more to come.
2569 :    
2570 : maechler 871 2005-08-18 Douglas Bates <bates@wisc.edu>
2571 : maechler 868
2572 : maechler 1174 * DESCRIPTION (Version): 0.98-5 released to CRAN
2573 : maechler 871
2574 :     * src/dgTMatrix.c (graphNEL_as_dgTMatrix): add first graphNEL methods
2575 :     * .....
2576 :    
2577 : bates 863 2005-08-18 Douglas Bates <bates@localhost.localdomain>
2578 :    
2579 :     * R/lmer.R: Corrected naming scheme in mcmcsamp to work with lmer
2580 :     or glmer objects.
2581 :    
2582 : maechler 860 2005-08-17 Martin Maechler <maechler@stat.math.ethz.ch>
2583 :    
2584 :     * DESCRIPTION (Version): 0.98-4 : upload to CRAN
2585 :    
2586 :     2005-08-16 Douglas Bates <bates@localhost.localdomain>
2587 :    
2588 :     * R/HBMM.R: finish re-writing R-only code.
2589 :    
2590 : bates 854 2005-08-15 Douglas Bates <bates@localhost.localdomain>
2591 :    
2592 :     * man/externalFormats.Rd: move documentation for writeHB and
2593 :     writeMM here.
2594 :    
2595 :     * src/mmio.c: replace inclusion of <malloc.h> by <stdlib.h>
2596 :     (suggested by Paul Roecker).
2597 :    
2598 :     * tests/validObj.R (assertError): Comment out test that is failing
2599 :     after recent changes in r-devel.
2600 :    
2601 : maechler 860
2602 : maechler 848 2005-08-11 Martin Maechler <maechler@stat.math.ethz.ch>
2603 :    
2604 :     * R/AllClass.R: intermediate virtual class "denseMatrix"
2605 :     * man/denseMatrix-class.Rd
2606 :     * NAMESPACE: export it, and also export
2607 :     * man/unused-classes.Rd: "iMatrix", "zMatrix" and "ldenseMatrix"
2608 :    
2609 : bates 846 2005-08-10 Douglas Bates <bates@wisc.edu>
2610 :    
2611 : maechler 848 * DESCRIPTION (Version): 0.98-3 to CRAN
2612 :    
2613 : bates 846 * src/dtrMatrix.c (dtrMatrix_validate): fixed up validation and
2614 :     matrix_solve code (which was really, really wrong).
2615 :    
2616 : bates 835 2005-08-07 Douglas Bates <bates@wisc.edu>
2617 : maechler 834
2618 :     * DESCRIPTION (Version): 0.98-2
2619 :    
2620 :     * R/HBMM.R (readHB), (readMM): read Matrix Market formats
2621 :    
2622 :     * R/lmer.R (abbrvNms): new
2623 :     * R/lmer.R (mcmcsamp): allow transformed parameters
2624 : bates 835 * src/HBMM.c (Matrix_writeMatrixMarket): Added read/write routines
2625 :     for the Harwell-Boeing and the MatrixMarket formats.
2626 : maechler 834
2627 :     2005-08-04 Martin Maechler <maechler@stat.math.ethz.ch>
2628 :    
2629 :     * man/dtrMatrix-class.Rd: add examples
2630 : bates 835 * man/dtpMatrix-class.Rd: ditto; plus note about PROBLEM
2631 : maechler 834
2632 :     * TODO: note the dtpMatrix (docu) bug
2633 :    
2634 :     * R/zzz.R (.onLoad): assignInNamespace("as.matrix", *, "base")
2635 :     in order to ensure that new as.matrix() is used by old functions,
2636 :     e.g., svd(), qr(), eigen(), dist(),..;
2637 :     apply(), also matplot() or pairs().
2638 :    
2639 :    
2640 :     2005-08-03 Martin Maechler <maechler@stat.math.ethz.ch>
2641 :    
2642 :     * R/lmer.R: add 'fixme' comments and move the linear vs glm check;
2643 :     add comments about 'control' / lmerControl() arguments
2644 :    
2645 : bates 835 2005-07-27 Douglas Bates <bates@wisc.edu>
2646 : bates 820
2647 : bates 835 * man/sleepstudy.Rd: Added the sleep data set.
2648 : maechler 1174 * DESCRIPTION (Version): 0.98-1 released to CRAN
2649 : bates 820
2650 : bates 835 2005-07-12 Douglas Bates <bates@wisc.edu>
2651 : maechler 834 * man/sleepstudy.Rd: Added the sleep data set.
2652 :    
2653 : bates 809 * R/lmer.R (glmmMCMC): Added PACKAGE = "Matrix" in a couple of
2654 :     .Call calls that were producing spurious output.
2655 :    
2656 : bates 835 2005-07-05 Douglas Bates <bates@wisc.edu>
2657 : bates 801
2658 :     * R/lmer.R (lmer): stored updated variance component estimates in
2659 :     mer object for the generalized model. (Bug reported by Renaud
2660 :     Lancelot).
2661 :    
2662 : bates 835 2005-07-03 Douglas Bates <bates@wisc.edu>
2663 : bates 794
2664 :     * src/lmer.c (glmer_devAGQ): Added AGQ for single grouping factor,
2665 :     unidimensional case.
2666 :    
2667 : bates 835 2005-06-08 Douglas Bates <bates@wisc.edu>
2668 : maechler 791
2669 :     * DESCRIPTION (Version): 0.96-1
2670 :    
2671 : maechler 1174 * moved lmer-class' R and C code moved from lme4 to here
2672 : maechler 791
2673 : bates 835 2005-06-04 Douglas Bates <bates@wisc.edu>
2674 : bates 763
2675 :     * R/dgCMatrix.R: Call to csc_matrix_mm used undefined arguments
2676 :     (reported by Guissepe Ragusa <gragusa@ucsd.edu>)
2677 :    
2678 : bates 835 2005-06-02 Douglas Bates <bates@wisc.edu>
2679 : bates 763
2680 :     * src/Makefile.win: Forgot to update this when Makefile changed.
2681 :    
2682 : bates 835 2005-05-11 Douglas Bates <bates@wisc.edu>
2683 : bates 726
2684 :     * src/dgCMatrix.c (csc_transpose): Simplified function fixing a
2685 :     bug reported by Kurt Hornik and Michael Hahsler.
2686 :    
2687 : bates 835 2005-05-10 Douglas Bates <bates@wisc.edu>
2688 : bates 725
2689 :     * src/lgCMatrix.c (Matrix_lgClgCmm): Implementation of methods for
2690 :     logical sparse matrices. These will also be used in the symbolic
2691 :     analysis for lmer objects.
2692 :    
2693 :     * src/dsCMatrix.c (dsCMatrix_matrix_solve): Copied the dimensions
2694 :     of b to the result. Fixes bug reported by Jean.Coursol@math.u-psud.fr
2695 : maechler 791
2696 : bates 835 2005-05-06 Douglas Bates <bates@wisc.edu>
2697 : bates 714
2698 :     * src/dgeMatrix.c (dgeMatrix_colsums): Added an implementation of
2699 :     colMeans, colSums, rowMeans and rowSums.
2700 :    
2701 : bates 835 2005-04-18 Douglas Bates <bates@wisc.edu>
2702 : bates 692
2703 :     * src/lgCMatrix.[ch]: code for _validate method and stub for
2704 :     multiplication operation.
2705 :    
2706 :     * src/dgeMatrix.c (dgeMatrix_matrix_solve): Passing wrong argument
2707 :     to dgetrs.
2708 :    
2709 :     * src/init.c: Fix cut-and-paste error in definition of
2710 :     dgeMatrix_matrix_solve
2711 :    
2712 :     * src/{many files}: Tighten code by using ALLOC_SLOT.
2713 :    
2714 : bates 835 2005-04-15 Douglas Bates <bates@wisc.edu>
2715 : bates 692
2716 :     * R/AllClass.R: Add lgTMatrix and lgCMatrix classes
2717 :    
2718 :     * DESCRIPTION: Eliminate import of stats.
2719 :    
2720 : maechler 791
2721 : bates 835 2005-04-06 Douglas Bates <bates@wisc.edu>
2722 : bates 692
2723 :     * R/AllClass.R : add logical sparse matrix classes
2724 :    
2725 : maechler 687 2005-04-01 Martin Maechler <maechler@stat.math.ethz.ch>
2726 :    
2727 :     * R/dgTMatrix.R: add "[" method for triplet matrices
2728 :     * R/sparseMatrix.R: and other sparse ones; --> add show() for sparse
2729 :    
2730 : bates 835 2005-03-31 Douglas Bates <bates@wisc.edu>
2731 : maechler 687
2732 :     * DESCRIPTION (Version): release 0.95-5 to CRAN
2733 :    
2734 :     * R/dMatrix.R: add %*%, crossprod and solve "fallback" methods
2735 :     * R/sparseMatrix.R: %*%, crossprod()
2736 :     * R/dgeMatrix.R: more "fallback" methods for numeric/dense matrices
2737 :     * man/*.Rd: move method definitions to 'Matrix' and 'dMatrix'
2738 :     * src/lmer.c (lmer_fitted): fix thinko
2739 :    
2740 : maechler 676 2005-03-26 Martin Maechler <maechler@stat.math.ethz.ch>
2741 :    
2742 :     * R/AllClass.R: add two virtual sparse classes ``on top''
2743 :    
2744 :     2005-03-24 Martin Maechler <maechler@stat.math.ethz.ch>
2745 :    
2746 :     * R/AllClass.R (setClass): use "VIRTUAL" for the virtual classes;
2747 :     correspondingly fix examples and tests/ since new()
2748 :     doesn't work for virtual classes.
2749 :    
2750 : maechler 658 2005-03-17 Martin Maechler <maechler@stat.math.ethz.ch>
2751 :    
2752 :     * R/Matrix.R (as.matrix): method and one for unname()
2753 :     * tests/dpoMatrix.R: tests should now be less platform dependent;
2754 :     also run for R 2.1.0; using as.matrix()
2755 :    
2756 : bates 835 2005-03-15 Douglas Bates <bates@wisc.edu>
2757 : maechler 658
2758 :     * R/pMatrix.R: "pMatrix" class added
2759 :     * ....
2760 :    
2761 : bates 835 2005-03-14 Douglas Bates <bates@wisc.edu>
2762 : bates 645
2763 :     * R/dtpMatrix.R: Add unpack method and an example.
2764 :    
2765 :     * src/dsyMatrix.c (dsyMatrix_trf): Add BunchKaufman factorization
2766 :     of general symmetric matrices and associated S4 methods.
2767 :    
2768 : maechler 658 2005-03-10 Martin Maechler <maechler@stat.math.ethz.ch>
2769 :     +
2770 :     2005-03-05 Martin Maechler <maechler@stat.math.ethz.ch>
2771 :    
2772 :     * R/dgeMatrix.R (setAs): and many other files: more coercion,
2773 :     crossprod() and "%*%" methods added; tests, too.
2774 :     * tests/matprod.R: new, for testing these
2775 :    
2776 : bates 835 2005-03-03 Douglas Bates <bates@wisc.edu>
2777 : bates 599
2778 :     * src/lmer.c (lmer_fitted): Added.
2779 :    
2780 : bates 835 2005-03-02 Douglas Bates <bates@wisc.edu>
2781 : bates 596
2782 :     * R/dsTMatrix.R: Conversion from dsTMatrix to dsCMatrix
2783 :    
2784 : bates 835 2005-02-28 Douglas Bates <bates@wisc.edu>
2785 : bates 582
2786 :     * src/*.c,po/,inst/po: Internationalization and localization of
2787 :     the package.
2788 :    
2789 :     * src/ldl.[ch]: Removed these as their contents are referenced in the
2790 :     R_ldl.c file.
2791 :    
2792 :     * src/flame.[ch]: Removed these source files.
2793 : maechler 658
2794 : bates 582 * src/dtrMatrix.c (make_array_triangular): Move to Mutils
2795 :    
2796 :     * src/LU.[ch],src/init.c: absorb in factorizations
2797 :    
2798 :     * src/Mutils.h: prepare for internationalization
2799 :    
2800 :     * src/cblas.h: move the enum definitions to Mutils.h and remove
2801 :     this file
2802 :    
2803 : maechler 578 2005-02-26 Martin Maechler <maechler@stat.math.ethz.ch>
2804 :    
2805 : maechler 579 * R/dgeMatrix.R: provide "dimnames" and "dimnames<-" methods
2806 :    
2807 :     * R/dtrMatrix.R: fix t() method
2808 :    
2809 : maechler 578 * R/dgeMatrix.R: define group methods "Arith", "Math", "Math2"
2810 : maechler 658 * NAMESPACE: export them (and import generics from "methods")
2811 : maechler 578 * tests/group-methods.R : and test them.
2812 :    
2813 :     * src/dtrMatrix.c (dtrMatrix_as_dgeMatrix): prevent seg.fault in
2814 :     border case
2815 :    
2816 :     2005-02-24 Douglas Bates <bates@stat.wisc.edu>
2817 :    
2818 : maechler 658 * DESCRIPTION (Version): 0.95-2 released to CRAN
2819 : maechler 578
2820 :     * src/dgBCMatrix.c:
2821 :     * src/lmer.c: many changes
2822 :     * ...
2823 :    
2824 : maechler 512 2005-02-04 Martin Maechler <maechler@stat.math.ethz.ch>
2825 :    
2826 :     * R/Matrix.R: add more sophisticated show() method.
2827 :    
2828 : maechler 578 2005-02-02 Douglas Bates <bates@stat.wisc.edu>
2829 :    
2830 :     * */* : almost complete reorganization of classes.
2831 :    
2832 : bates 835 2005-01-26 Douglas Bates <bates@wisc.edu>
2833 : bates 460
2834 :     * R/AllGeneric.R: Added matrix exponential generic expm and a method
2835 :     for the geMatrix class.
2836 :    
2837 : bates 835 2005-01-24 Douglas Bates <bates@wisc.edu>
2838 : bates 460
2839 :     * src/Makefile (clean): Remove *.a and *.so
2840 :    
2841 :     * man/cscBlocked-class.Rd: Remove reference to the lmer-class.
2842 :    
2843 : bates 835 2005-01-23 Douglas Bates <bates@wisc.edu>
2844 : bates 460
2845 : maechler 658 * src/lmer.c (Lind): Definition of Lind was backwards. This only
2846 : bates 460 had an effect in cases with more than 2 grouping factors.
2847 :    
2848 : bates 835 2005-01-03 Douglas Bates <bates@wisc.edu>
2849 : bates 415
2850 :     * src/lmeRep.c (lmer_variances): change from lmeRep to lmer
2851 :    
2852 : bates 835 2004-12-23 Douglas Bates <bates@wisc.edu>
2853 : bates 410
2854 :     * src/init.c (R_init_Matrix): Reorder calls to R_registerRoutines
2855 :     and R_useDynamicSymbols (suggested by B.D.Ripley).
2856 :    
2857 : bates 835 2004-12-14 Douglas Bates <bates@wisc.edu>
2858 : bates 392
2859 :     * R/sscMatrix.R: Add determinant methods
2860 :    
2861 :     * src/triplet.[ch],src/init.c (triplet_to_matrix): Add a coercion
2862 :     for tripletMatrix to matrix.
2863 :    
2864 : bates 835 2004-12-13 Douglas Bates <bates@wisc.edu>
2865 : bates 388
2866 : bates 392 * R/AllClass.R (.onLoad): Eliminate the bbCrosstab class, which is
2867 :     no longer used.
2868 :    
2869 : bates 388 * src/R_ldl.c: Created an R-specific version of the ldl.[ch] files
2870 :     with dynamic allocation of scratch arrays.
2871 :    
2872 :     * src/ssclme.c (ssclme_copy_ctab): Fixed bug in creation of ZtZ
2873 :     for multivariate random effects with multiple grouping factors.
2874 :     Fixes part but not all of #15.
2875 :    
2876 : bates 835 2004-12-03 Douglas Bates <bates@wisc.edu>
2877 : bates 375
2878 :     * src/lmeRep.c (lmeRep_factor): order of operations for multiple
2879 :     scalar grouping factors corrected.
2880 :    
2881 : bates 835 2004-11-29 Douglas Bates <bates@wisc.edu>
2882 : bates 375
2883 :     * src/bCrosstab.c: remove diag_update which is no longer used
2884 :    
2885 : bates 835 2004-11-16 Douglas Bates <bates@wisc.edu>
2886 : bates 350
2887 :     * src/Metis_utils.c: Move metis.h include to C sources so that the
2888 :     .h file can be included.
2889 :    
2890 : bates 835 2004-11-12 Douglas Bates <bates@wisc.edu>
2891 : bates 342
2892 : bates 350 * src/LU.c,geMatrix.c,trMatrix.c, etc.:
2893 : bates 342 Complete allocation of slots in NEW_OBJECT.
2894 :    
2895 :     * src/Mutils.h: Moved list of symbols to an include file
2896 :    
2897 : bates 835 2004-11-11 Douglas Bates <bates@wisc.edu>
2898 : bates 342
2899 :     * src/geMutils.c (Matrix_init): remove unused function
2900 :    
2901 : bates 835 2004-11-10 Douglas Bates <bates@wisc.edu>
2902 : bates 342
2903 :     * src/cscMatrix.c (csc_to_imagemat): removed unused function
2904 :    
2905 : bates 835 2004-11-05 Douglas Bates <bates@wisc.edu>
2906 : bates 327
2907 :     * src/Makefile.win (SOURCES_C): Keep consistent with Makefile
2908 :    
2909 : bates 835 2004-10-27 Douglas Bates <bates@wisc.edu>
2910 : bates 303
2911 :     * R/pdmatrix.R: remove PACKAGE="Matrix" in .Call calls
2912 :    
2913 : bates 835 2004-10-04 Douglas Bates <bates@wisc.edu>
2914 : bates 296
2915 :     * src/init.c: Created R_init_Matrix and added registration of C
2916 :     routines.
2917 :    
2918 : bates 835 2004-10-02 Douglas Bates <bates@wisc.edu>
2919 : bates 283
2920 :     * R/tripletMatrix.R: Force a require(lattice) for the image methods.
2921 :    
2922 : bates 835 2004-06-15 Douglas Bates <bates@wisc.edu>
2923 : bates 229
2924 :     * man/trMatrix-class.Rd: Escape the % chars in .Rd files.
2925 :    
2926 : bates 111 2004-04-20 Douglas Bates <bates@stat.wisc.edu>
2927 :    
2928 :     * src/Makefile.win ($(SHLIB)): Modifications per Uwe Ligges.
2929 :    
2930 : bates 109 2004-04-19 Douglas Bates <bates@stat.wisc.edu>
2931 :    
2932 :     * src/ssclme.c (ssclme_update_mm): fix logic error in
2933 :     ssclme_update_mm
2934 :    
2935 : bates 105 2004-04-18 Douglas Bates <bates@stat.wisc.edu>
2936 :    
2937 :     * src/ssclme.c (ssclme_coef, ssclme_coefGets): Create consistency
2938 :     in the order of unconstrained and constrained parameters.
2939 :     (ssclme_gradient): Added the gradients (not yet correct for
2940 :     multidimensional, unconstrained case).
2941 :    
2942 : bates 78 2004-04-14 Douglas Bates <bates@stat.wisc.edu>
2943 :    
2944 :     * src/ssclme.c (ssclme_EMsteps): Fix logic in REML update
2945 :    
2946 :     * src/Makefile.win: Remove unneeded ranlib call
2947 :    
2948 : bates 71 2004-04-12 Douglas Bates <bates@stat.wisc.edu>
2949 :    
2950 :     * DESCRIPTION (Version): New release
2951 :    
2952 :     * src/Makefile.win: Update Makefile.win to umfpack removal.
2953 :    
2954 : bates 49 2004-04-05 Douglas Bates <bates@bates2_home>
2955 :    
2956 :     * src/triplet_to_col.c: Create triplet_to_col as a native
2957 : maechler 658 function, not the version from umfpack. There were problems with
2958 : bates 49 the configuration of UMFPACK for 64-bit processors and there was
2959 :     only one umfpack routine being used so I moved it here.
2960 :    
2961 : bates 45 2004-04-04 Douglas Bates <bates@bates2_home>
2962 :    
2963 :     * src/ssclme.c (ssclme_variances): New function.
2964 :    
2965 : bates 28 2004-03-28 Douglas Bates <bates@bates2_home>
2966 :    
2967 :     * src/ssclme.c (ssclme_fitted): Added function.
2968 :    
2969 : bates 22 2004-03-27 Douglas Bates <bates@bates2_home>
2970 :    
2971 :     * src/ssclme.c (ssclme_transfer_dimnames): Add new function to
2972 :     store the dimnames in the XtX and bVar slots
2973 :     (ssclme_update_mm): Change the dimensions of the bVar slot
2974 :     components and the returned value from ssclme_ranef.
2975 :    
2976 : bates 10 2004-03-18 Douglas Bates <bates@stat.wisc.edu>
2977 :    
2978 :     * R/{pdMat.R,pdIdent.R,pdLogChol.R,pdMatrixLog.R,pdNatural.R},
2979 :     src/{pdMat.c,pdIdent.c,pdLogChol.c,pdNatural.c},
2980 :     tests/{pdCompSymm.R,pdDiag.R,pdIdent.R,pdLogChol.R,pdNatural.R},
2981 :     man/{pdMat-class.Rd,pdmatrix-class.Rd,corrmatrix-class.Rd,
2982 :     pdDiag-class.Rd,pdIdent-class.Rd,pdNatural-class.Rd,
2983 :     pdLogChol-class.Rd,coefGets.Rd,pdCompSymm-class.Rd,
2984 :     pdfactor-class.Rd,pdFactor.Rd,pdMatrix.Rd,
2985 :     pdBlocked-class.Rd},AllClass.R,AllGeneric.R:
2986 :     Moved the pdMat classes from the lme4 package.
2987 :    
2988 :     2004-03-02 Douglas Bates <bates@stat.wisc.edu>
2989 :    
2990 :     * man/ssclme-class.Rd: Update definition and documentation of the
2991 :     ssclme class to include the DIsqrt slot.
2992 :    
2993 :     * src/ssclme.c (ssclme_deviance): Modify order of computation
2994 :     (much faster using dsyrk, a level 3 BLAS routine).
2995 :    
2996 :     * src/Makefile (SUBLIBS): Change definition (K. Hornik)
2997 :    
2998 :     2004-02-28 Douglas Bates <bates@stat.wisc.edu>
2999 :    
3000 :     * tests/ssclme.R: Modify the test to account for the permutation
3001 :     of the levels of the grouping factors.
3002 :    
3003 :     2004-02-23 Douglas Bates <bates@stat.wisc.edu>
3004 :    
3005 :     * R/ssclme.R,src/ssclme.c (ssclme): Move slots of sscCrosstab slot
3006 :     directly into the ssclme class definition.
3007 :    
3008 :     2004-02-22 Douglas Bates <bates@stat.wisc.edu>
3009 :    
3010 :     * DESCRIPTION (Date): New release
3011 :    
3012 :     * man/ssclme-class.Rd: new file.
3013 :    
3014 :     * src/ssclme.c (ssclme_loglik): major revisions in design. It
3015 :     works and it's fast!
3016 :    
3017 :     2004-02-17 Douglas Bates <bates@stat.wisc.edu>
3018 :    
3019 :     * src/taucs/Makefile.win (lib): Change "ar" to "$(AR)" (B.Ripley)
3020 :    
3021 :     2004-02-16 Douglas Bates <bates@stat.wisc.edu>
3022 :    
3023 :     * DESCRIPTION (Date): New release
3024 :    
3025 :     * NAMESPACE: Don't export ssclme.
3026 :    
3027 :     * data/ScotsSec.rda, man/ScotsSec.Rd: Add Scottish secondary
3028 :     school data.
3029 :    
3030 :     2004-02-11 Douglas Bates <bates@stat.wisc.edu>
3031 :    
3032 :     * src/sscCrosstab.c (sscCrosstab): Added a row to the incidence to
3033 :     keep track of the fixed-effects and the response. Counts also
3034 :     gets an extra element, which is always one.
3035 :    
3036 :     * src/ldl.c: Include these routines from Tim Davis' LDL package.
3037 :    
3038 :     2004-02-10 Douglas Bates <bates@stat.wisc.edu>
3039 :    
3040 :     * src/cscMatrix.c (csc_transpose): new function
3041 :    
3042 :     * src/Mutils.c (csc_sort_columns): perm/iperm confusion corrected
3043 :     (csc_components_transpose): new function
3044 :    
3045 :     2004-02-06 Douglas Bates <bates@stat.wisc.edu>
3046 :    
3047 :     * src/triplet.c (triplet_validate): Fix Dim slot on generated
3048 :     triplets
3049 :    
3050 :     2004-01-30 Douglas Bates <bates@stat.wisc.edu>
3051 :    
3052 :     * R/sscCrosstab.R (sscCrosstab): Added sscCrosstab generator function.
3053 :    
3054 :     * src/LU.h (MATRIX_LU_H): Add #ifndef #define ... #endif to this
3055 :     and all other .h files in src.
3056 :    
3057 :     * src/Makefile.win: This and other Makefile.win files contributed
3058 :     by Brian Ripley.
3059 :    
3060 :     2004-01-27 Douglas Bates <bates@stat.wisc.edu>
3061 :    
3062 :     * R/syMatrix.R: Added methods for "%*%".
3063 :    
3064 :     * R/Hilbert.R (Hilbert): Changed Hilbert function to return a
3065 :     poMatrix object.
3066 :    
3067 :     2004-01-26 Douglas Bates <bates@stat.wisc.edu>
3068 :    
3069 :     * man/sscChol-class.Rd,man/mm.Rd,man/y.Rd: Added man pages.
3070 :    
3071 :     2004-01-25 Douglas Bates <bates@bates2_home>
3072 :    
3073 :     * inst/doc/Introduction.Rnw,Comparisons.Rnw: Added vignettes.
3074 :    
3075 :     * R/csc.R: Convert all cscMatrix classes to use Dim slot instead
3076 :     of nrow.
3077 :    
3078 :     2003-12-31 Douglas Bates <bates@stat.wisc.edu>
3079 :    
3080 :     * src/taucs/taucs.h: Moved taucs.h, amd.h, and umfpack.h into
3081 :     subdirectories.
3082 :    
3083 :     2003-12-08 Douglas Bates <bates@stat.wisc.edu>
3084 :    
3085 :     * src/taucs.h: Accidently referred to global header files
3086 :     instead of local files.
3087 :    
3088 :     2003-12-04 Douglas Bates <bates@stat.wisc.edu>
3089 :    
3090 :     * R/AllClass.R: Lots of changes. Removed all the lapack++ code
3091 :     and methods and replaced all classes with S4 classes.
3092 :    
3093 :     2003-04-19 Douglas Bates <bates@stat.wisc.edu>
3094 :    
3095 :     * R/det.R,man/det.Rd: Change name of det generic to determinant
3096 :    
3097 :     * src/R_LapackPP.cc: Change method of calculating determinants
3098 :    
3099 :     2003-02-03 Douglas Bates <bates@stat.wisc.edu>
3100 :    
3101 :     * DESCRIPTION (Version): removed empty data directory as requested
3102 :     by CRAN maintainers. Changed version number and date.
3103 :    
3104 :     2002-10-23 Douglas Bates <bates@stat.wisc.edu>
3105 :    
3106 :     * src/laindex.h: Applied patches from Brian Ripley for compilation
3107 :     under Windows.
3108 :    
3109 :     * Added configure.win and src/Makevars.win as requested by Brian
3110 :     Ripley.
3111 :    
3112 :     2002-05-03 Douglas Bates <bates@stat.wisc.edu>
3113 :    
3114 :     * src/lamatrix.h: Removing pre-1.2.0 compatibility code per Kurt
3115 :     Hornik.
3116 :    
3117 :     2002-04-24 Douglas Bates <bates@stat.wisc.edu>
3118 :    
3119 :     * configure.ac: Replaced configure.in with configure.ac
3120 :     contributed by Kurt Hornik.
3121 :    
3122 :     * aclocal.m4 (ac_clean_files): Replaced this with Kurt Hornik's
3123 :     version for R-1.5.0
3124 :    
3125 : maechler 512
3126 : bates 10 2001-12-10 Douglas Bates <bates@stat.wisc.edu>
3127 :    
3128 :     * man/eigen.Rd: Removed the .Alias in the example

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