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revision 1852, Mon May 21 16:42:35 2007 UTC revision 2185, Sat Apr 26 20:33:16 2008 UTC
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1    2008-04-26  Martin Maechler  <maechler@stat.math.ethz.ch>
2    
3            * inst/test-tools.R (checkMatrix): test <Ops> not only for dMatrix
4            * R/Ops.R: more methods, for lMatrix/nMatrix
5    
6    2008-04-24  Martin Maechler  <maechler@stat.math.ethz.ch>
7    
8            * R/expm.R: new file for all expm() methods; notably new ones for
9            diagonal*, triangular*, symmetric* and also simple "matrix".
10    
11    2008-04-23  Martin Maechler  <maechler@stat.math.ethz.ch>
12    
13            * R/dsyMatrix.R: setAs(.) rather than setIs(.)  "to dpoMatrix"
14    
15            * inst/test-tools.R (assert.EQ.mat): better message when not equal
16    
17            * src/dgeMatrix.c (dgeMatrix_matrix_crossprod): allow integer RHS.
18    
19            * R/AllClass.R (ddiMatrix,ldiMatrix): extend [dl]Matrix instead of
20            [dl]denseMatrix {identical slots; but more logical method dispatch}
21    
22    2008-04-23  Martin Maechler  <maechler@stat.math.ethz.ch>
23    
24            * R/sparseMatrix.R (summary): use length(<i-slot>) instead of nnzero()
25    
26            * R/diagMatrix.R (determinant): method
27    
28    2008-04-22  Martin Maechler  <maechler@stat.math.ethz.ch>
29    
30            * src/dsCMatrix.c (dsCMatrix_Cholesky): suppress CHOLMOD printing too
31    
32            * R/Rsparse.R (.viaC.to.R): uplo fix for symmetric & triangular
33    
34            * R/dsCMatrix.R (determinant): switch to use Cholesky( 'LDL' ) and
35            its diagonal
36    
37    2008-04-21  Martin Maechler  <maechler@stat.math.ethz.ch>
38    
39            * R/dMatrix.R (Summary): short-cut for prod(<sparse>)
40    
41            * R/not.R: fix !<"U"-diag-ltrMatrix> ; drop {R < 2.6.0}-branch
42    
43            * R/Auxiliaries.R (tT2gT): fix for "U"-diag-ltTMatrix
44    
45            * R/AllClass.R: ltTMatrix validity: call (more stringent) tTMatrix_validate
46    
47    2008-04-19  Martin Maechler  <maechler@stat.math.ethz.ch>
48    
49            * R/Ops.R (Ops.x.x): aux.function, not just for (dMatrix,dMatrix)
50    
51            * R/Ops.R (.do.Logic.lsparse): fix NA case
52    
53            * R/Tsparse.R (replTmat): fix r.sym case, using indTri()
54    
55            * R/Auxiliaries.R (nnzero): fix special cases, using
56            * R/Auxiliaries.R (indDiag): new utility
57            * R/Auxiliaries.R (indTri): new argument 'diag'
58    
59            * R/dMatrix.R: Summmary(<ddenseMatrix>): different branch for dsy*
60    
61    2008-04-18  Martin Maechler  <maechler@stat.math.ethz.ch>
62    
63            * R/diagMatrix.R: "Summary" methods, and more "Arith" / "Ops"
64    
65            * src/Csparse.c (Csparse_drop): preserve (uplo,diag) for
66            ".tCMatrix" triangular matrix.
67    
68            * R/Auxiliaries.R (drop0): use diagU2N(); according to helpfile,
69            'clx' can be class *or* class representation.
70            (nnzSparse): new.
71            (non0ind): new 'xtendSymm' argument; used in
72            * R/Ops.R:
73    
74            * R/pMatrix.R: more efficient determinant() method
75    
76    2008-04-17  Martin Maechler  <maechler@stat.math.ethz.ch>
77    
78            * [disactivated] R/Matrix.R (det): det() as base::det(), but with Matrix environment
79            * [disactivated] NAMESPACE: export(det)
80    
81            * R/diagMatrix.R (mkDiag): new substitute for diag()
82    
83            * R/Auxiliaries.R (nnzero): fix for "diagU2N"-case
84            (as0, as1): new utility.
85    
86            * R/Csparse.R (diag, band): need diagU2N()
87    
88            * src/dgeMatrix.c (get_norm): return NA when 'x' slot has NA/NaN.
89    
90            * R/lMatrix.R: coerce(nMatrix |-> lMatrix) fix
91    
92            * R/Ops.R (Compare): fix <nsp> o <nsp> case
93    
94            * R/nsparseMatrix.R, R/pMatrix.R: is.na() method
95    
96    2008-04-16  Martin Maechler  <maechler@stat.math.ethz.ch>
97    
98            * R/Auxiliaries.R (signPerm): new utility for
99            * R/Auxiliaries.R (detSparseLU): determinant() via sparseLU
100    
101            * src/dsCMatrix.c (dsCMatrix_LDL_D): suppress 'CHOLMOD warning';
102            since we have our own error handler (and can use tryCatch() from R).
103    
104    2008-04-15  Martin Maechler  <maechler@stat.math.ethz.ch>
105    
106            * R/dgTMatrix.R (image): ha! set col=NA if lwd is small -- very nice!
107    
108            * R/dsCMatrix.R (determinant): use tryCatch() and switch to lu()
109            when not positive definite.
110    
111            * R/Auxiliaries.R (asTri): new auxiliary
112            (non0.i): make *much* faster for Tsparse with many non-zero
113            entries; add 'uniqT = TRUE' argument to be used when sorting is undesired.
114    
115            * tests/Class+Meth.R (dotestMat): now build on checkMatrix() from
116            test-tools.R , see below
117    
118            * R/dMatrix.R: fix "Summary" method: + diagU2N()
119    
120            * NAMESPACE, R/Matrix.R: add mean() method
121    
122    2008-04-12  Martin Maechler  <maechler@stat.math.ethz.ch>
123    
124            * R/dgTMatrix.R (image): allow to *not* take abs(), and use
125            cold-hot colors; try *changed* default useAbs = FALSE
126            * man/image-methods.Rd:  nice examples
127    
128    2008-04-11  Martin Maechler  <maechler@stat.math.ethz.ch>
129    
130            * inst/test-tools.R (checkMatrix): new function for modularizing part
131            of tstMatrixClass() in tests/Class+Meth.R
132    
133            * R/dsCMatrix.R: coercion from "matrix"
134            * R/ltTMatrix.R, R/ntTMatrix.R: ditto (change it).
135    
136            * tests/Class+Meth.R (tstMatrixClass): some cleanup;
137            add test for as(matrix(,0,0), <class>)
138    
139    2008-04-09  Martin Maechler  <maechler@stat.math.ethz.ch>
140    
141            * src/dgeMatrix.c (dgeMatrix_determinant): for n == 0,
142            work as determinant(matrix(,0,0)).
143    
144            * src/dgCMatrix.c (dgCMatrix_LU): return {L,U} as dtCMatrix
145            * man/sparseLU-class.Rd: ditto
146    
147            * R/dgCMatrix.R (determinant): method building on lu()
148            * R/sparseMatrix.R, Matrix.R, ...: ditto
149    
150            * R/Auxiliaries.R (mkDet): auxiliary for determinant()
151    
152    2008-04-07  Martin Maechler  <maechler@stat.math.ethz.ch>
153    
154            * R/sparseMatrix.R (summary<sparseMatrix>): no 'x' column for
155            pattern matrices.
156    
157    2008-04-02  Martin Maechler  <maechler@stat.math.ethz.ch>
158    
159            * src/dense.c (dense_to_Csparse): all declarations *before*
160            R_CheckStack(); needed e.g. for ancient gcc 2.96.
161    
162    
163    2008-03-29  Martin Maechler  <maechler@stat.math.ethz.ch>
164    
165            * DESCRIPTION (Version): 0.999375-9 --- need to release
166            for R-devel (and R 2.7.0 alpha soon).
167    
168            * R/AllClass.R: drop "double" from "atomicVector" class union
169    
170            * R/AllGeneric.R (rcond): check for base::rcond instead of R version
171            * R/dgeMatrix.R: ditto
172    
173            * R/sparseMatrix.R (summary): count NAs
174    
175            * inst/doc/Intro2Matrix.Rnw: changes, aim for *one* introduction.
176    
177    2008-03-28  Martin Maechler  <maechler@stat.math.ethz.ch>
178    
179            * R/AllGeneric.R: rcond(., norm) instead of rcond(., type), in
180            order to become compatible to new R 2.7.0 base::rcond().
181    
182    2008-03-25  Martin Maechler  <maechler@stat.math.ethz.ch>
183    
184            * DESCRIPTION (Version,Date): 0.999375-8 --- released to CRAN
185    
186            * R/diagMatrix.R (Ops): fix newly introduce bug in <.di> o <numeric>
187    
188            * inst/test-tools.R (isValid): new utility, used much in
189            * tests/simple.R:
190    
191            * man/BunchKaufman-methods.Rd: added too
192    
193    2008-03-24  Martin Maechler  <maechler@stat.math.ethz.ch>
194    
195            * R/dsyMatrix.R: add BunchKaufman() methods.
196            * R/dspMatrix.R:
197    
198            * src/init.c: add dsyMatrix_trf
199    
200    2008-03-23  Douglas Bates <bates@stat.wisc.edu>
201    
202            * DESCRIPTION (Version): release 0.999375-7
203            * src/CHMfactor.c (CHMfactor_update): fix
204    
205    2008-03-22  Martin Maechler  <maechler@stat.math.ethz.ch>
206    
207            * src/dsCMatrix.c (dsCMatrix_LDL_D): cleanup, also using
208            internal_chm_factor().
209    
210            * R/AllGeneric.R: do *not* define a "chol" generic
211                    (but rather use the implicit one *without* making pivot
212                    part of the signature)
213            * R/*.R: drop the 'pivot' from chol's signature and make
214                    'pivot=FALSE' a default argument of method definitions.
215    
216            * .Rbuildignore: add 'wrld_1deg': I.e. do not put it into released
217            version of Matrix
218    
219    2008-03-18  Martin Maechler  <maechler@stat.math.ethz.ch>
220    
221            * R/Tsparse.R (.T.2.n): drop 0's before coercion to "nMatrix"
222    
223            * R/sparseMatrix.R (is.na): new simple method
224            * R/denseMatrix.R (is.na): ditto.
225    
226            * R/diagMatrix.R (.symDiagonal): newly exported utility.
227    
228            * R/diagMatrix.R (Ops): <diag> * <numeric> should not become dgeMatrix!
229    
230            * src/UFsparse_download.sh: -->
231            * src/CHOLMOD/: update to CHOLMOD version 1.6 (Nov.2007)
232    
233    2008-03-17  Martin Maechler  <maechler@stat.math.ethz.ch>
234    
235            * src/dsCMatrix.c (dsCMatrix_LDL_D): even faster utility with same
236            functionality; barely tested in
237            * tests/factorizing.R
238    
239            * src/Csparse.c (diag_tC): new functionality to enable faster
240            determinant(<dsCMatrix>, .) in
241            * R/dsCMatrix.R
242    
243    2008-03-17 18:53  Douglas Bates <bates@stat.wisc.edu>
244    
245            * R/CHMfactor.R, inst/include/Matrix.h, inst/include/Matrix_stubs.c,
246              src/CHMfactor.c, src/CHMfactor.h,
247              man/CHMfactor-class.Rd, src/init.c, tests/factorizing.R:
248              Log-determinant of the parent matrix from a CHMfactor object as
249              chm_factor_ldetL2; documentation and support
250    
251    2008-03-15  Martin Maechler  <maechler@stat.math.ethz.ch>
252    
253            * R/dsCMatrix.R: enable determinant(<dsCMatrix>, .) via chol(.)
254    
255    2008-03-14  Martin Maechler  <maechler@stat.math.ethz.ch>
256    
257            * R/dsCMatrix.R: setAs(., "dsCMatrix") but with a deprecation
258            warning.
259    
260    2008-03-13  Martin Maechler  <maechler@stat.math.ethz.ch>
261    
262            * DESCRIPTION (Version, Date): bug-fix release 0.999375-6
263    
264            * R/diagMatrix.R (diag2tT.u): utility to be smarter in
265              <diagonal> o <sparse_triangular>
266              setAs(., "nMatrix") added.
267    
268            * R/diagMatrix.R (Diagonal): Diagonal(4, x=3) now works too
269    
270            * R/Auxiliaries.R (.diagU2N): more careful coercion in 2 steps
271                    new argument 'checkDense = FALSE'.
272    
273    
274    2008-03-07  Martin Maechler  <maechler@stat.math.ethz.ch>
275    
276            * src/dgeMatrix.c (dgeMatrix_exp): fix the octave-origin bug in the
277            back-permutation of the matrix exponential.
278    
279            * tests/matr-exp.R: test the fix (for an example where expm() was wrong).
280    
281            * DESCRIPTION (Date,Version): ready to release 0.999375-5
282    
283            * tests/simple.R: testing diagN2U
284    
285    2008-03-06  Martin Maechler  <maechler@stat.math.ethz.ch>
286    
287            * R/Auxiliaries.R (diagN2U): interface to
288    
289            * src/Csparse.c (Csparse_diagN2U): .Call()able SEXP version of chm_diagN2U()
290    
291            * tests/matprod.R: test for triangularity preserving <dtC> %*% <dtC>
292    
293    2008-03-05  Martin Maechler  <maechler@stat.math.ethz.ch>
294    
295            * src/chm_common.c (chm_diagN2U): new utility.
296    
297            * src/Csparse.c (Csparse_Csparse_crossprod, Csparse_Csparse_prod):
298            make use of chm_diagN2U() and hence now preserve triangularity and
299            unit-triangularity.
300    
301            * DESCRIPTION (LicenseDetails): new; such that 'License:' becomes "canonical"
302    
303    2008-03-04  Martin Maechler  <maechler@stat.math.ethz.ch>
304    
305            * R/diagMatrix.R (subDiag): fix when x[..] became a vector
306    
307            * src/Tsparse.c (Tsparse_diagU2N): new utility, necessary for e.g.
308            * src/Csparse.c (Csparse_crossprod): use [CT]sparse_diagU2N() !!
309    
310            * R/Auxiliaries.R (.diagU2N): make use of new Tsparse_diagU2N
311    
312            * R/Ops.R ("-" (<sparseMatrix>)): use diagU2N()
313    
314            * src/chm_common.c (AS_CHM_FINISH): add note about problem
315            for triangular (diag = "U").
316    
317    2008-02-21  Martin Maechler  <maechler@stat.math.ethz.ch>
318    
319            * R/Auxiliaries.R (as_Csparse2): drop this, replacing by
320            * R/bind.R:  .Call(dense_to_Csparse, *)
321    
322    2008-02-20  Martin Maechler  <maechler@stat.math.ethz.ch>
323    
324            * R/Matrix.R (Matrix): no longer use coercions to specific classes
325                    (since we are discouraging them in user code).
326    
327            * tests/*.R: also replaces coercions to specific classes by
328            coercions to super classes.
329    
330            * R/denseMatrix.R (.dense2C): simplified by using forceSymmetric()
331    
332    
333    2008-02-19  Martin Maechler  <maechler@stat.math.ethz.ch>
334    
335            * man/CAex.Rd: example: coerce to symmetric*, not dsC*
336    
337            * src/dense.c (dense_band): generalized from ddense_band
338    
339            * R/ddenseMatrix.R (.trilDense,.triuDense, .bandDense):
340              now for "denseMatrix" (instead of just "ddense*"); much
341              simplified setMethod()s for these.
342    
343            * src/dense.c (dense_to_symmetric): generalized from ddense_*
344    
345    2008-02-18  Martin Maechler  <maechler@stat.math.ethz.ch>
346    
347            * R/AllGeneric.R: forceSymmetric() generic: fast no-checking
348            version of as(*, "symmetricMatric").
349    
350            * src/dense.c (ddense_to_symmetric): add 'symm_test' argument, and
351            * R/symmetricMatrix.R: set it TRUE in coercion to "symmetricMatrix"
352    
353    2008-02-16  Martin Maechler  <maechler@stat.math.ethz.ch>
354    
355            * R/Matrix.R (subset.ij): utility, as first step to faster
356               M [ <ij-matrix> ] indexing.
357    
358            * R/Matrix.R (.M.sub.i.logical): M[ <logical> ] : try better.
359    
360            * src/dense.c (ddense_symmpart, ddense_skewpart): new functions
361            for more efficient symmpart() and skewpart() methods.
362    
363            * src/Mutils.c (equal_string_vectors): utility
364    
365            * src/dense.c (ddense_to_symmetric): new function used in
366    
367            * R/symmetricMatrix.R: setAs(., "symmetricMatrix")
368    
369            * R/sparseMatrix.R, et_al (isSymmetric): add '...' to formals, in
370            order to match the generic (and evade .local(..)).
371    
372            * R/dsCMatrix.R: dgC -> dsC: use C code!
373    
374            * NAMESPACE, R/AllGeneric.R (symmpart, skewpart): new functions
375            as per TODO
376    
377            * R/Auxiliaries.R (setZero, all0Matrix): new utilities
378    
379            * R/symmetricMatrix.R: obvious symmpart(), skewpart() methods
380    
381    
382    2008-02-15  Martin Maechler  <maechler@stat.math.ethz.ch>
383    
384            * R/Ops.R (.Arith.Csparse): use diagU2N when needed in triangular
385    
386            * R/Auxiliaries.R (non0.i): take out of non0ind
387    
388            * R/ddenseMatrix.R (.trilDense, .triuDense, .bandDense):
389            make tril(), triu(), band() work for "matrix" and all "dense*"
390    
391            * R/triangularMatrix.R (.tri[lu].tr): need .diagU2N(*)
392            * tests/simple.R: test the fix above
393    
394            * R/sparseMatrix.R ([): simplification: no coerce to <general>
395                    before we use as(., <Tsparse>)[...] anyway
396    
397            * R/Rsparse.R (.viaC.to.R): mostly instead of .viaC.to.dgR()
398    
399            * R/triangularMatrix.R (isTriangular): methods for all subclasses
400            instead of "triangularMatrix" -- just to disambiguate
401    
402    2008-02-14  Martin Maechler  <maechler@stat.math.ethz.ch>
403    
404            * tests/Class+Meth.R (dotestMat): add m[FALSE, FALSE] { <-> TODO}
405            * tests/indexing.R: example that fails above
406    
407    2008-01-26  Martin Maechler  <maechler@stat.math.ethz.ch>
408    
409            * R/Matrix.R (.M.sub.i.2col): fix for logical matrix indexing
410            * R/Tsparse.R (.TM.sub.i.2col, .TM.repl.i.2col): ditto;
411                    now, M[lower.tri(M)] and  M[lower.tri(M)] <- v  work better
412    
413            * src/Tsparse.c (Tsparse_to_tCsparse): new fast utility.
414            * src/Tsparse.h, init.c: ditto
415            * R/Auxiliaries.R (isTriT): new; faster than going via Csparse
416                 both isTriC() and isTriT() now return TRUE with "kind" or FALSE.
417            * R/sparseMatrix.R (isTriangular): hence simplified
418    
419    2008-01-24  Martin Maechler  <maechler@stat.math.ethz.ch>
420    
421            * R/Ops.R (.Arith.Csparse): new utility factored out of former
422              <dgC> o <dgC>, extended for triangular and also used in  <dtC> o <dtC>.
423    
424    2008-01-23  Martin Maechler  <maechler@stat.math.ethz.ch>
425    
426            * tests/factorizing.R (checkSchur): and more tests for checking Schur()
427    
428            * inst/test-tools.R (isOrthogonal): new function; also file restructured
429    
430    2008-01-22  Martin Maechler  <maechler@stat.math.ethz.ch>
431    
432            * R/ngTMatrix.R: allow as(<numeric matrix>, "ngTMatrix") and hence
433            coercion to "nMatrix" and "pMatrix"
434    
435            * R/AllClass.R: "Schur" class;  "number" class union
436            * man/number-class.Rd:
437            * man/Schur-class.Rd:
438    
439            * R/eigen.R (.dgeSchur): utility, and return "Schur" class
440            (.simpleSchur): Schur() method for diagonal matrices
441            (.triSchur):    Schur() method for triangular matrices
442            (Schur.sym):    Schur() for symmetric matrices {building on eigen()}.
443    
444    
445    2008-01-21  Martin Maechler  <maechler@stat.math.ethz.ch>
446    
447            * src/dgCMatrix.c (dgCMatrix_QR): set @Dim slot (as per doc)
448    
449    2008-01-15  Martin Maechler  <maechler@stat.math.ethz.ch>
450    
451            * R/CHMfactor.R (solve): method for b="numeric", but also b="ANY"
452                    in order to ensure 'system = *' is not lost;
453                    formals()$system instead of cut&paste.
454            * tests/factorizing.R: test solve(<CHM..>, <numeric>)
455    
456    2008-01-11  Martin Maechler  <maechler@stat.math.ethz.ch>
457    
458            * DESCRIPTION (Date): make ready for release --> 0.999375-4
459    
460            * R/dgeMatrix.R: fix rcond() method for "dgeMatrix".
461    
462    2007-12-08  Martin Maechler  <maechler@stat.math.ethz.ch>
463    
464            * R/pMatrix.R: as(*, "matrix") now returns 0/1 *integer* matrix,
465                    and hence does as.vector(.).
466            * man/pMatrix-class.Rd: docs
467            * R/sparseMatrix.R: fix for printing "integer sparse"
468    
469            * tests/Class+Meth.R (tstMatrixClass): test M[FALSE], M[2] etc
470    
471            * R/Matrix.R and others: use "exact" function argument list for
472                    both "["   : (x, i,j, ..., drop)
473                    and  "[<-" : (x, i,j, ..., value)
474    
475            * R/denseMatrix.R: M[i] and M[i] <- v  (i vector) now work
476            * R/Tsparse.R (replTmat):    ditto
477            * R/diagMatrix.R (replDiag): ditto
478            * R/Csparse.R (replCmat):    ditto {was it worth the pain?}
479            * tests/indexing.R: testing the above
480    
481    2007-12-07  Martin Maechler  <maechler@stat.math.ethz.ch>
482    
483            * R/sparseMatrix.R (cov2cor): method for sparse matrices
484    
485            * R/diagMatrix.R ([<-): fix   D[ cbind(i,j) ] <- v
486    
487            * R/bind2.R: fix for Rsparse* and rbind2(dense,dense)
488    
489            * tests/Class+Meth.R: test cbind2, rbind2  and  diag<-
490    
491    2007-12-06  Martin Maechler  <maechler@stat.math.ethz.ch>
492    
493            * R/Matrix.R: "generic" cov2cor() method
494    
495            * R/nearPD.R: new 'only.values', 'keepDiag' arguments;
496                    speed up Q %*% D %*% t(Q)
497            * tests/dpoMatrix.R: test nearPD()
498    
499    2007-12-05  Doug Bates and Martin Maechler
500    
501            * R/sparseMatrix.R: xtabs(*, sparse=.) function; an extention of
502            stats::xtabs() allowing to create sparse matrices.
503    
504    2007-10-08  Martin Maechler  <maechler@stat.math.ethz.ch>
505    
506            * DESCRIPTION (Version): *-4 (released *-3 two days ago)
507    
508    2007-10-06  Martin Maechler  <maechler@stat.math.ethz.ch>
509    
510            * R/pMatrix.R: solve(<Matrix>, <pMatrix>)
511    
512    2007-10-05  Martin Maechler  <maechler@stat.math.ethz.ch>
513    
514            * R/LU.R: solve() method for "denseLU"
515    
516    2007-10-01  Martin Maechler  <maechler@stat.math.ethz.ch>
517    
518            * DESCRIPTION (Version): 0.999375-3 preparing for release
519    
520            * R/AllGeneric.R: simplify  if(.) .. else .. for R <= 2.5.1
521    
522            * R/Matrix.R (Matrix): .Internal(matrix(..)) different for R >= 2.7.0
523    
524    2007-09-26  Martin Maechler  <maechler@stat.math.ethz.ch>
525    
526            * R/pMatrix.R (.m.mult.pMat): fix <matrix> %*% <pMatrix>,
527              thanks to Kasper Kristensen.
528            * tests/matprod.R: regression test for that.
529    
530    2007-09-23 17:32  Douglas Bates <bates@stat.wisc.edu>
531    
532            * [r4778] R/AllGeneric.R: Check R version before defining generics for
533              primitives
534    
535    2007-09-13  Martin Maechler  <maechler@stat.math.ethz.ch>
536    
537            * R/denseMatrix.R (rcond): method
538            * R/sparseQR.R (rcond): method, use x or t(x)
539    
540    2007-09-12  Martin Maechler  <maechler@stat.math.ethz.ch>
541    
542            * R/dgeMatrix.R (rcond): method: work via qr.R() for non-square
543            matrices.
544            * R/sparseMatrix.R: Ditto for all other rcond() method definitions.
545    
546            * man/rcond.Rd: mention the more general definition, and add
547            example for non-square matrices.
548    
549            * man/chol.Rd: new file, for the S4 chol() generic and all methods.
550    
551    2007-09-11  Martin Maechler  <maechler@stat.math.ethz.ch>
552    
553            * R/sparseQR.R: add qr.R() method [to be used for rcond()]
554    
555    2007-09-01  Martin Maechler  <maechler@stat.math.ethz.ch>
556    
557            * R/Matrix.R ([<-): add (Matrix,missing,ANY,Matrix) etc
558            * tests/indexing.R: add new regression for the above cases.
559    
560    2007-08-30  Martin Maechler  <maechler@stat.math.ethz.ch>
561    
562            * src/Mutils.h (__sun): clause for alloca.h on Solaris
563    
564    2007-08-16  Martin Maechler  <maechler@stat.math.ethz.ch>
565    
566            * DESCRIPTION (Date, Version): 0.999375-2
567    
568    2007-08-15  Martin Maechler  <maechler@stat.math.ethz.ch>
569    
570            * R/HBMM.R (readMM): make work for pattern matrices as well
571    
572    2007-08-14 13:07  Douglas Bates <bates@stat.wisc.edu>
573    
574            * [r4730] src/Mutils.h: declare alloca
575            * [r4734] NAMESPACE, R/AllGeneric.R, R/Csparse.R, R/HBMM.R, R/Tsparse.R,
576              R/dgCMatrix.R, R/dgTMatrix.R, R/dsCMatrix.R, R/dsTMatrix.R,
577              man/externalFormats.Rd, src/Csparse.c, src/Csparse.h, src/DEPS.mkf,
578              src/HBMM.c, src/HBMM.h, src/Mutils.h, src/SOURCES_C.mkf, src/init.c,
579              src/mmio.c, src/mmio.h: Remove deprecated function writeHB and its
580              methods; switch writeMM to use CHOLMOD code; repair readMM
581    
582    2007-08-14  Martin Maechler  <maechler@stat.math.ethz.ch>
583    
584            * R/nearPD.R, man/nearPD.Rd (nearPD): new function built on Jens
585            Oehlschlaegel's ... result type still to be discussed!
586    
587    2007-08-10  Martin Maechler  <maechler@stat.math.ethz.ch>
588    
589            * man/image-methods.Rd: new, combining all image() methods
590    
591    2007-08-09  Martin Maechler  <maechler@stat.math.ethz.ch>
592    
593            * R/dgCMatrix.R: define qr() and lu() methods for "sparseMatrix"
594            to work via dgC...
595    
596            * R/Matrix.R (Matrix): special treatment for "table" (S3)
597    
598    2007-08-07  Martin Maechler  <maechler@stat.math.ethz.ch>
599    
600            * R/dgTMatrix.R (image): change defaults to
601                    aspect = "iso", colorkey = FALSE
602    
603    2007-08-06  Martin Maechler  <maechler@stat.math.ethz.ch>
604    
605            * src/dsyMatrix.c (dsyMatrix_matrix_mm): 'b' might be matrix;
606            must copy its *expanded* x slot before LAPACK call.
607    
608            * tests/matprod.R: test the last days' changes.
609    
610    2007-08-06 16:43  Douglas Bates <bates@stat.wisc.edu>
611    
612            * [r4712] inst/include/Matrix_stubs.c: Change R_cholmod_printf in stubs
613              as well as in sources
614            * [r4713] src/dsyMatrix.c: Duplicate the contents of the RHS before
615              Lapack call
616    
617    2007-08-03  Martin Maechler  <maechler@stat.math.ethz.ch>
618    
619            * R/Matrix.R (%*%, crossprod, tcrossprod): add method for
620                    ("Matrix", "matrix") which is needed in some cases.
621            Ditto for solve().
622    
623            * R/colSums.R (.as.dge.Fun): need ddenseMatrix methods to avoid
624            infinite recursion in dispatch for some cases.
625    
626    2007-08-02 08:48  Martin Maechler <maechler@stat.math.ethz.ch>
627    
628            * [r4693] src/chm_common.c: R_cholmod_printf() instead of Rprintf() just
629              so pointers match
630    
631    2007-08-02  Martin Maechler  <maechler@stat.math.ethz.ch>
632    
633            * DESCRIPTION (Date): set ready for release -- 0.999375-1
634    
635    2007-08-01 15:44  Douglas Bates <bates@stat.wisc.edu>
636    
637            * [r4686] inst/include/Matrix.h, inst/include/Matrix_stubs.c,
638              src/chm_common.c, src/chm_common.h: Change API for
639              numeric_as_chm_dense and N_AS_CHM_DN
640    
641    2007-08-01  Martin Maechler  <maechler@stat.math.ethz.ch>
642    
643            * src/dtrMatrix.c (dtrMatrix_matrix_mm): fix dimensionality check (!)
644            * tests/matprod.R: regr.test for it
645    
646    2007-07-20  Martin Maechler  <maechler@stat.math.ethz.ch>
647    
648            * R/dMatrix.R: fix from Brian for   Math2(., digits = "missing")
649            * tests/group-methods.R: and regression-test it
650    
651    2007-07-19 19:45  Douglas Bates <bates@stat.wisc.edu>
652    
653            * [r4642] inst/include/Matrix.h, inst/include/Matrix_stubs.c,
654              inst/include/cholmod.h, src/chm_common.c, src/init.c: Export
655              triplet_to_sparse, documentation, use typedefs
656    
657    2007-07-18  Martin Maechler  <maechler@stat.math.ethz.ch>
658    
659            * man/dpoMatrix-class.Rd: added 'corMatrix' example
660    
661            * src/dsyMatrix.[ch] (dsyMatrix_as_matrix): new 'keep_dimnames' arg
662            * src/dtrMatrix.[ch] (dtrMatrix_as_matrix): ditto
663            * src/init.c, R/dsyMatrix.R, R/dtrMatrix.R, R/lgTMatrix.R: ditto
664    
665            * R/lsparseMatrix.R: bug fix in "all" method
666            * R/Ops.R (.do.Logic.lsparse): "|" bug in borderline case
667    
668            * R/dsyMatrix.R (coerce->dsTMatrix): (i,j) slots should *not* have names
669            * R/ngTMatrix.R (coerce->ngTMatrix): ditto;
670                    + matrix |-> nMatrix coercion
671            * R/pMatrix.R: + setAs()  to dMatrix and from nMatrix
672            * man/pMatrix-class.Rd: ditto
673    
674            * R/Matrix.R (Summary): method for non-dMatrix
675    
676            * tests/Class+Meth.R (extraValid): new check about "dirty" slots
677            * tests/Class+Meth.R (tstMatrixClass): test norm(.);
678                    test all Summary methods.
679    
680    2007-07-16  Martin Maechler  <maechler@stat.math.ethz.ch>
681    
682            * R/dgeMatrix.R (norm, rcond): methods for 'matrix'
683    
684    2007-07-14  Martin Maechler  <maechler@stat.math.ethz.ch>
685    
686            * R/sparseMatrix.R (norm): simple methods for sparseMatrix
687    
688            * R/pMatrix.R (t?crossprod): methods for pMatrix
689    
690    2007-07-10  Douglas Bates  <bates@stat.wisc.edu>
691    
692            * src/dgeMatrix.c (dgeMatrix_colsums): Get the logic straight.
693    
694    2007-07-09 20:45  Douglas Bates <bates@stat.wisc.edu>
695    
696            * [r4579] src/dgeMatrix.c: Untangle horrible code in dgeMatrix_colsums
697              trying to fix a subtle bug - which has been somewhere else.
698    
699    2007-07-09 19:43  Martin Maechler <maechler@stat.math.ethz.ch>
700    
701            * [r4578] src/dgeMatrix.c: "cleaned" dgeMatrix_colsums() - but did not
702              solve the bug
703    
704    2007-07-08  Martin Maechler  <maechler@stat.math.ethz.ch>
705    
706            * src/dgCMatrix.c (compressed_to_TMatrix):
707    
708    2007-07-07  Martin Maechler  <maechler@stat.math.ethz.ch>
709    
710            * src/Csparse.c (Rsparse_validate): new, to have some validity
711            checking for RsparseMatrix
712            * src/dgCMatrix.c (xRMatrix_validate): ditto
713            * src/dtCMatrix.c (tRMatrix_validate): ditto
714    
715    2007-07-07  Douglas Bates <bates@stat.wisc.edu>
716    
717            * [r4567] R/AllClass.R: Slots already in RsparseMatrix were redefined in
718              lgRMatrix
719            * [r4568] DESCRIPTION: Prepare for bug-fix release
720            * [r4570] src/CHOLMOD/Check/cholmod_write.c: Include cholmod_matrixops.h
721              for declaration of cholmod_symmetry
722    
723    2007-07-06  Martin Maechler  <maechler@stat.math.ethz.ch>
724    
725            * DESCRIPTION (Version): 0.999375 merged into the trunk; ready for
726            release.
727    
728    2007-07-06 14:11  Douglas Bates <bates@stat.wisc.edu>
729    
730            * [r4559] src/iohb.c, src/iohb.h: Remove Harwell-Boeing input/output
731              functions - no longer used
732            * [r4560] src/HBMM.c, src/Mutils.c, src/dgTMatrix.c, src/dgeMatrix.c,
733              src/dspMatrix.c, src/dsyMatrix.c, src/dtCMatrix.c,
734              src/factorizations.c, src/sparseQR.c: Replace most calls to Calloc by
735              Alloca
736    
737    2007-07-06 13:14  Martin Maechler <maechler@stat.math.ethz.ch>
738    
739            * [r4558] inst/doc/Comparisons.Rnw, src/CHMfactor.c, src/Csparse.c,
740              src/Tsparse.c, src/chm_common.c, src/chm_common.h, src/dense.c,
741              src/dgCMatrix.c, src/dsCMatrix.c, src/dtTMatrix.c, src/sparseQR.c,
742              src/t_gCMatrix_colSums.c: more R_CheckStack()s
743    
744    2007-07-05 18:12  Douglas Bates <bates@stat.wisc.edu>
745    
746            * [r4550] inst/include/Matrix.h: Add the macro N_AS_CHM_DN to "alloca"
747              the required amount of memory then call M_numeric_as_chm_dense.
748            * [r4556] src/Mutils.h, src/dgCMatrix.c: Define and use the Alloca macro
749              (like Calloc but calling alloca)
750    
751    2007-07-05  Martin Maechler  <maechler@stat.math.ethz.ch>
752    
753            * R/sparseMatrix.R (printSpMatrix): renamed from prSpMatrix()
754            and extended with more sophisticated 'col.names' option.
755            * NAMESPACE: export  printSparseMatrix()
756            * man/printSpMatrix.Rd: document, incl. examples
757    
758    2007-07-04 16:21  Douglas Bates <bates@stat.wisc.edu>
759    
760            * [r4543] src/cs_utils.c, src/cs_utils.h, src/dgCMatrix.c,
761              src/dtCMatrix.c, src/sparseQR.c: CSP typedef for *cs and macro
762              AS_CSP. API change - pass the empty structure to Matrix_as_cs.
763    
764    2007-07-04  Martin Maechler  <maechler@stat.math.ethz.ch>
765    
766            * DESCRIPTION (Version): 0.99875-4
767    
768            * tests/Class+Meth.R (tstMatrixClass): add dimnames, and hence test
769            some dimnames perservation.
770    
771            * R/dsTMatrix.R (t-method): keep dimnames
772            * R/dtTMatrix.R:  ditto
773    
774            * R/sparseMatrix.R (prSpMatrix): print colnames when non-trivial
775            and ncol(.) < 10
776    
777            * src/cs_utils.c: drop check_class() and use Matrix_check_class()
778            from Mutils.h
779    
780            * src/lgCMatrix.c ([ln]csc_to_matrix): no longer lose dimnames,
781            e.g. in as(<ngCMatrix>, "matrix")
782    
783    2007-07-01 13:27  Douglas Bates <bates@stat.wisc.edu>
784    
785            * [r4529] .: Create a branch for the API changes from the 0.99875
786              series to the 0.999375 series
787            * [r4530] DESCRIPTION, inst/include/Matrix.h,
788              inst/include/Matrix_stubs.c, src/CHMfactor.c, src/Csparse.c,
789              src/Mutils.h, src/Tsparse.c, src/chm_common.c, src/chm_common.h,
790              src/dense.c, src/dgCMatrix.c, src/dsCMatrix.c, src/dtTMatrix.c,
791              src/t_gCMatrix_colSums.c: API change - pass the empty structure to the
792              as_cholmod_x functions
793    
794    2007-06-30 09:05  Martin Maechler <maechler@stat.math.ethz.ch>
795    
796            * [r4527] trunk/Matrix/DESCRIPTION, trunk/Matrix/NAMESPACE,
797              trunk/Matrix/inst/doc/Comparisons.Rnw: add session- and hardware-info
798              to Comparisons
799    
800    >>>>>>> .merge-right.r4561
801    2007-06-29  Martin Maechler  <maechler@stat.math.ethz.ch>
802    
803            * DESCRIPTION (Version): 0.99875-3 ready to be released.
804    
805            * R/sparseMatrix.R (spMatrix): make spMatrix(3,4) working
806    
807            * R/AllGeneric.R: set "Math" (and "Math2") group generics in a way
808            that should also work in a future version of R.
809    
810    2007-06-21  Martin Maechler  <maechler@stat.math.ethz.ch>
811    
812            * NAMESPACE, R/AllClass.R: "xsparseVector" class union.
813    
814            * R/sparseVector.R: more *sparseVector coercions, notably for
815            non - double ones.
816    
817    2007-06-19  Martin Maechler  <maechler@stat.math.ethz.ch>
818    
819            * R/colSums.R: new file for all (col|row)(Sums|Means) methods,
820              notably the new ones building on the new .Call(.)s:
821    
822            * src/dgCMatrix.c (DEF_gCMatrix_COLSUMS): use to define
823            all 4 of [dlin]gCMatrix_colSums().
824    
825    2007-06-18 16:12  Douglas Bates <bates@stat.wisc.edu>
826    
827            * [r4472] src/Syms.h, src/init.c: Added Matrix_lengthSym
828            * [r4473] src/dgCMatrix.c: Modified dgCMatrix_colSums for sparseVector
829              result
830    
831    2007-06-16  Martin Maechler  <maechler@stat.math.ethz.ch>
832    
833            * R/kronecker.R: fix typo (could lead to inf.recursion)
834            * test/simple.R: testing that
835    
836            * R/sparseMatrix.R (prSpMatrix): change to be used as print()
837            method as well (which can have arguments, show() can't).
838    
839    2007-06-16 15:52  Douglas Bates <bates@stat.wisc.edu>
840    
841            * [r4466] R/dgCMatrix.R, src/dgCMatrix.c, src/dgCMatrix.h, src/init.c:
842              added dgCMatrix_colSums for [col,row][Sums,Means]
843    
844    2007-06-15 23:15  Douglas Bates <bates@stat.wisc.edu>
845    
846            * [r4460] R/sparseMatrix.R, man/dgCMatrix-class.Rd, src/dgCMatrix.c,
847              src/dgCMatrix.h, src/init.c: added lm.fit.sparse (unexported),
848              coercion of "factor" to "dgCMatrix" and dgCMatrix_cholsol
849            * [r4461] R/AllClass.R, man/sparseMatrix-class.Rd: draft "indicators"
850              class
851            * [r4463] R/sparseMatrix.R, man/dgCMatrix-class.Rd,
852              man/sparseMatrix-class.Rd: Don't need an "indicators" class - use the
853              row names to store the levels - duh!  Added an example.
854    
855    2007-06-14  Martin Maechler  <maechler@stat.math.ethz.ch>
856    
857            * src/Csparse.c (Csparse_validate): check for *repeated* entries
858            thanks to example from Christian Buchta; with a test here:
859            * tests/simple.R:
860    
861    2007-06-07  Martin Maechler  <maechler@stat.math.ethz.ch>
862    
863            * R/Auxiliaries.R (callGeneric): another fix, needed for some cases
864            of colSums(*, sparseResult = TRUE)
865    
866    2007-06-06  Martin Maechler  <maechler@stat.math.ethz.ch>
867    
868            * R/lsparseMatrix.R, R/ldenseMatrix.R (all, any): change default to
869            'na.rm = FALSE' as "everywhere" else in R.
870    
871    2007-06-05 Douglas Bates <bates@stat.wisc.edu>
872    
873            * [r4421] src/CSparse_install.sh: Modify for new organization of
874              CSparse package
875            * [r4425] src/UFsparse_download.sh: Update to version 3.0.0 of
876              SuiteSparse
877            * [r4426] src/Makefile: add ./UFconfig to the include path for
878              compilation
879            * [r4427] src/cs.[ch]: update to CSparse version 2.2.0
880            * [r4428] inst/doc/UFsparse/* src/{AMD,CHOLMOD,COLAMD}/*
881              src/UFconfig/UFconfig.h: Update to version 3.0.0 of SuiteSparse
882    
883    2007-06-05  Martin Maechler  <maechler@stat.math.ethz.ch>
884    
885            * R/Auxiliaries.R (emptyColnames): + argument msg.if.not.empty, used in
886            * R/sparseMatrix.R (prSpMatrix): now gives a message about
887            suppressed column names.
888    
889    2007-06-04 17:13  Douglas Bates <bates@stat.wisc.edu>
890    
891            * [r4418] src/Csparse.c, src/HBMM.c, src/Mutils.c, src/Mutils.h,
892              src/Tsparse.c, src/chm_common.c, src/chm_common.h, src/dgCMatrix.c,
893              src/dgeMatrix.c, src/dpoMatrix.c, src/dpoMatrix.h, src/dppMatrix.c,
894              src/dppMatrix.h, src/dsCMatrix.c, src/dspMatrix.c, src/dspMatrix.h,
895              src/dsyMatrix.c, src/dsyMatrix.h, src/dtpMatrix.c, src/dtrMatrix.c:
896              Remove warnings after change to const char* CHAR
897    
898    2007-06-04 17:11  Douglas Bates <bates@stat.wisc.edu>
899    
900            * [r4417] inst/include/Matrix_stubs.c, inst/include/cholmod.h: Corrected
901              type of M_cholmod_ssmult
902    
903    2007-06-03 14:42  Douglas Bates <bates@stat.wisc.edu>
904    
905            * [r4412] inst/include/Matrix_stubs.c, inst/include/cholmod.h,
906              src/init.c: Yet another cholmod export - cholmod_ssmult
907    
908    2007-05-23  Martin Maechler  <maechler@stat.math.ethz.ch>
909    
910            * NAMESPACE: exported drop0(), since
911            * man/drop0.Rd: I have seen several cases, I really wanted to use
912            it, so our users may want too.
913    
914    2007-05-22  Martin Maechler  <maechler@stat.math.ethz.ch>
915    
916            * man/colSums.Rd: separately document colSums() etc, since these
917            have the extra argument 'sparseResult'.
918    
919  2007-05-21  Martin Maechler  <maechler@stat.math.ethz.ch>  2007-05-21  Martin Maechler  <maechler@stat.math.ethz.ch>
920    
921          * R/sparseMatrix.R (spMatrix): utility (T)sparse Matrix constructor;          * R/sparseMatrix.R (spMatrix): utility (T)sparse Matrix constructor;

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