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revision 2105, Tue Jan 15 10:16:29 2008 UTC revision 2186, Mon Apr 28 12:37:01 2008 UTC
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1    2008-04-28  Martin Maechler  <maechler@stat.math.ethz.ch>
2    
3            * R/Tsparse.R ([): for triangularMatrix, check if result may be
4            triangular.
5            * tests/indexing.R: regression test
6    
7    2008-04-26  Martin Maechler  <maechler@stat.math.ethz.ch>
8    
9            * inst/test-tools.R (checkMatrix): test <Ops> not only for dMatrix
10            * R/Ops.R: more methods, for lMatrix/nMatrix
11    
12    2008-04-24  Martin Maechler  <maechler@stat.math.ethz.ch>
13    
14            * R/expm.R: new file for all expm() methods; notably new ones for
15            diagonal*, triangular*, symmetric* and also simple "matrix".
16    
17    2008-04-23  Martin Maechler  <maechler@stat.math.ethz.ch>
18    
19            * R/dsyMatrix.R: setAs(.) rather than setIs(.)  "to dpoMatrix"
20    
21            * inst/test-tools.R (assert.EQ.mat): better message when not equal
22    
23            * src/dgeMatrix.c (dgeMatrix_matrix_crossprod): allow integer RHS.
24    
25            * R/AllClass.R (ddiMatrix,ldiMatrix): extend [dl]Matrix instead of
26            [dl]denseMatrix {identical slots; but more logical method dispatch}
27    
28    2008-04-23  Martin Maechler  <maechler@stat.math.ethz.ch>
29    
30            * R/sparseMatrix.R (summary): use length(<i-slot>) instead of nnzero()
31    
32            * R/diagMatrix.R (determinant): method
33    
34    2008-04-22  Martin Maechler  <maechler@stat.math.ethz.ch>
35    
36            * src/dsCMatrix.c (dsCMatrix_Cholesky): suppress CHOLMOD printing too
37    
38            * R/Rsparse.R (.viaC.to.R): uplo fix for symmetric & triangular
39    
40            * R/dsCMatrix.R (determinant): switch to use Cholesky( 'LDL' ) and
41            its diagonal
42    
43    2008-04-21  Martin Maechler  <maechler@stat.math.ethz.ch>
44    
45            * R/dMatrix.R (Summary): short-cut for prod(<sparse>)
46    
47            * R/not.R: fix !<"U"-diag-ltrMatrix> ; drop {R < 2.6.0}-branch
48    
49            * R/Auxiliaries.R (tT2gT): fix for "U"-diag-ltTMatrix
50    
51            * R/AllClass.R: ltTMatrix validity: call (more stringent) tTMatrix_validate
52    
53    2008-04-19  Martin Maechler  <maechler@stat.math.ethz.ch>
54    
55            * R/Ops.R (Ops.x.x): aux.function, not just for (dMatrix,dMatrix)
56    
57            * R/Ops.R (.do.Logic.lsparse): fix NA case
58    
59            * R/Tsparse.R (replTmat): fix r.sym case, using indTri()
60    
61            * R/Auxiliaries.R (nnzero): fix special cases, using
62            * R/Auxiliaries.R (indDiag): new utility
63            * R/Auxiliaries.R (indTri): new argument 'diag'
64    
65            * R/dMatrix.R: Summmary(<ddenseMatrix>): different branch for dsy*
66    
67    2008-04-18  Martin Maechler  <maechler@stat.math.ethz.ch>
68    
69            * R/diagMatrix.R: "Summary" methods, and more "Arith" / "Ops"
70    
71            * src/Csparse.c (Csparse_drop): preserve (uplo,diag) for
72            ".tCMatrix" triangular matrix.
73    
74            * R/Auxiliaries.R (drop0): use diagU2N(); according to helpfile,
75            'clx' can be class *or* class representation.
76            (nnzSparse): new.
77            (non0ind): new 'xtendSymm' argument; used in
78            * R/Ops.R:
79    
80            * R/pMatrix.R: more efficient determinant() method
81    
82    2008-04-17  Martin Maechler  <maechler@stat.math.ethz.ch>
83    
84            * [disactivated] R/Matrix.R (det): det() as base::det(), but with Matrix environment
85            * [disactivated] NAMESPACE: export(det)
86    
87            * R/diagMatrix.R (mkDiag): new substitute for diag()
88    
89            * R/Auxiliaries.R (nnzero): fix for "diagU2N"-case
90            (as0, as1): new utility.
91    
92            * R/Csparse.R (diag, band): need diagU2N()
93    
94            * src/dgeMatrix.c (get_norm): return NA when 'x' slot has NA/NaN.
95    
96            * R/lMatrix.R: coerce(nMatrix |-> lMatrix) fix
97    
98            * R/Ops.R (Compare): fix <nsp> o <nsp> case
99    
100            * R/nsparseMatrix.R, R/pMatrix.R: is.na() method
101    
102    2008-04-16  Martin Maechler  <maechler@stat.math.ethz.ch>
103    
104            * R/Auxiliaries.R (signPerm): new utility for
105            * R/Auxiliaries.R (detSparseLU): determinant() via sparseLU
106    
107            * src/dsCMatrix.c (dsCMatrix_LDL_D): suppress 'CHOLMOD warning';
108            since we have our own error handler (and can use tryCatch() from R).
109    
110    2008-04-15  Martin Maechler  <maechler@stat.math.ethz.ch>
111    
112            * R/dgTMatrix.R (image): ha! set col=NA if lwd is small -- very nice!
113    
114            * R/dsCMatrix.R (determinant): use tryCatch() and switch to lu()
115            when not positive definite.
116    
117            * R/Auxiliaries.R (asTri): new auxiliary
118            (non0.i): make *much* faster for Tsparse with many non-zero
119            entries; add 'uniqT = TRUE' argument to be used when sorting is undesired.
120    
121            * tests/Class+Meth.R (dotestMat): now build on checkMatrix() from
122            test-tools.R , see below
123    
124            * R/dMatrix.R: fix "Summary" method: + diagU2N()
125    
126            * NAMESPACE, R/Matrix.R: add mean() method
127    
128    2008-04-12  Martin Maechler  <maechler@stat.math.ethz.ch>
129    
130            * R/dgTMatrix.R (image): allow to *not* take abs(), and use
131            cold-hot colors; try *changed* default useAbs = FALSE
132            * man/image-methods.Rd:  nice examples
133    
134    2008-04-11  Martin Maechler  <maechler@stat.math.ethz.ch>
135    
136            * inst/test-tools.R (checkMatrix): new function for modularizing part
137            of tstMatrixClass() in tests/Class+Meth.R
138    
139            * R/dsCMatrix.R: coercion from "matrix"
140            * R/ltTMatrix.R, R/ntTMatrix.R: ditto (change it).
141    
142            * tests/Class+Meth.R (tstMatrixClass): some cleanup;
143            add test for as(matrix(,0,0), <class>)
144    
145    2008-04-09  Martin Maechler  <maechler@stat.math.ethz.ch>
146    
147            * src/dgeMatrix.c (dgeMatrix_determinant): for n == 0,
148            work as determinant(matrix(,0,0)).
149    
150            * src/dgCMatrix.c (dgCMatrix_LU): return {L,U} as dtCMatrix
151            * man/sparseLU-class.Rd: ditto
152    
153            * R/dgCMatrix.R (determinant): method building on lu()
154            * R/sparseMatrix.R, Matrix.R, ...: ditto
155    
156            * R/Auxiliaries.R (mkDet): auxiliary for determinant()
157    
158    2008-04-07  Martin Maechler  <maechler@stat.math.ethz.ch>
159    
160            * R/sparseMatrix.R (summary<sparseMatrix>): no 'x' column for
161            pattern matrices.
162    
163    2008-04-02  Martin Maechler  <maechler@stat.math.ethz.ch>
164    
165            * src/dense.c (dense_to_Csparse): all declarations *before*
166            R_CheckStack(); needed e.g. for ancient gcc 2.96.
167    
168    
169    2008-03-29  Martin Maechler  <maechler@stat.math.ethz.ch>
170    
171            * DESCRIPTION (Version): 0.999375-9 --- need to release
172            for R-devel (and R 2.7.0 alpha soon).
173    
174            * R/AllClass.R: drop "double" from "atomicVector" class union
175    
176            * R/AllGeneric.R (rcond): check for base::rcond instead of R version
177            * R/dgeMatrix.R: ditto
178    
179            * R/sparseMatrix.R (summary): count NAs
180    
181            * inst/doc/Intro2Matrix.Rnw: changes, aim for *one* introduction.
182    
183    2008-03-28  Martin Maechler  <maechler@stat.math.ethz.ch>
184    
185            * R/AllGeneric.R: rcond(., norm) instead of rcond(., type), in
186            order to become compatible to new R 2.7.0 base::rcond().
187    
188    2008-03-25  Martin Maechler  <maechler@stat.math.ethz.ch>
189    
190            * DESCRIPTION (Version,Date): 0.999375-8 --- released to CRAN
191    
192            * R/diagMatrix.R (Ops): fix newly introduce bug in <.di> o <numeric>
193    
194            * inst/test-tools.R (isValid): new utility, used much in
195            * tests/simple.R:
196    
197            * man/BunchKaufman-methods.Rd: added too
198    
199    2008-03-24  Martin Maechler  <maechler@stat.math.ethz.ch>
200    
201            * R/dsyMatrix.R: add BunchKaufman() methods.
202            * R/dspMatrix.R:
203    
204            * src/init.c: add dsyMatrix_trf
205    
206    2008-03-23  Douglas Bates <bates@stat.wisc.edu>
207    
208            * DESCRIPTION (Version): release 0.999375-7
209            * src/CHMfactor.c (CHMfactor_update): fix
210    
211    2008-03-22  Martin Maechler  <maechler@stat.math.ethz.ch>
212    
213            * src/dsCMatrix.c (dsCMatrix_LDL_D): cleanup, also using
214            internal_chm_factor().
215    
216            * R/AllGeneric.R: do *not* define a "chol" generic
217                    (but rather use the implicit one *without* making pivot
218                    part of the signature)
219            * R/*.R: drop the 'pivot' from chol's signature and make
220                    'pivot=FALSE' a default argument of method definitions.
221    
222            * .Rbuildignore: add 'wrld_1deg': I.e. do not put it into released
223            version of Matrix
224    
225    2008-03-18  Martin Maechler  <maechler@stat.math.ethz.ch>
226    
227            * R/Tsparse.R (.T.2.n): drop 0's before coercion to "nMatrix"
228    
229            * R/sparseMatrix.R (is.na): new simple method
230            * R/denseMatrix.R (is.na): ditto.
231    
232            * R/diagMatrix.R (.symDiagonal): newly exported utility.
233    
234            * R/diagMatrix.R (Ops): <diag> * <numeric> should not become dgeMatrix!
235    
236            * src/UFsparse_download.sh: -->
237            * src/CHOLMOD/: update to CHOLMOD version 1.6 (Nov.2007)
238    
239    2008-03-17  Martin Maechler  <maechler@stat.math.ethz.ch>
240    
241            * src/dsCMatrix.c (dsCMatrix_LDL_D): even faster utility with same
242            functionality; barely tested in
243            * tests/factorizing.R
244    
245            * src/Csparse.c (diag_tC): new functionality to enable faster
246            determinant(<dsCMatrix>, .) in
247            * R/dsCMatrix.R
248    
249    2008-03-17 18:53  Douglas Bates <bates@stat.wisc.edu>
250    
251            * R/CHMfactor.R, inst/include/Matrix.h, inst/include/Matrix_stubs.c,
252              src/CHMfactor.c, src/CHMfactor.h,
253              man/CHMfactor-class.Rd, src/init.c, tests/factorizing.R:
254              Log-determinant of the parent matrix from a CHMfactor object as
255              chm_factor_ldetL2; documentation and support
256    
257    2008-03-15  Martin Maechler  <maechler@stat.math.ethz.ch>
258    
259            * R/dsCMatrix.R: enable determinant(<dsCMatrix>, .) via chol(.)
260    
261    2008-03-14  Martin Maechler  <maechler@stat.math.ethz.ch>
262    
263            * R/dsCMatrix.R: setAs(., "dsCMatrix") but with a deprecation
264            warning.
265    
266    2008-03-13  Martin Maechler  <maechler@stat.math.ethz.ch>
267    
268            * DESCRIPTION (Version, Date): bug-fix release 0.999375-6
269    
270            * R/diagMatrix.R (diag2tT.u): utility to be smarter in
271              <diagonal> o <sparse_triangular>
272              setAs(., "nMatrix") added.
273    
274            * R/diagMatrix.R (Diagonal): Diagonal(4, x=3) now works too
275    
276            * R/Auxiliaries.R (.diagU2N): more careful coercion in 2 steps
277                    new argument 'checkDense = FALSE'.
278    
279    
280    2008-03-07  Martin Maechler  <maechler@stat.math.ethz.ch>
281    
282            * src/dgeMatrix.c (dgeMatrix_exp): fix the octave-origin bug in the
283            back-permutation of the matrix exponential.
284    
285            * tests/matr-exp.R: test the fix (for an example where expm() was wrong).
286    
287            * DESCRIPTION (Date,Version): ready to release 0.999375-5
288    
289            * tests/simple.R: testing diagN2U
290    
291    2008-03-06  Martin Maechler  <maechler@stat.math.ethz.ch>
292    
293            * R/Auxiliaries.R (diagN2U): interface to
294    
295            * src/Csparse.c (Csparse_diagN2U): .Call()able SEXP version of chm_diagN2U()
296    
297            * tests/matprod.R: test for triangularity preserving <dtC> %*% <dtC>
298    
299    2008-03-05  Martin Maechler  <maechler@stat.math.ethz.ch>
300    
301            * src/chm_common.c (chm_diagN2U): new utility.
302    
303            * src/Csparse.c (Csparse_Csparse_crossprod, Csparse_Csparse_prod):
304            make use of chm_diagN2U() and hence now preserve triangularity and
305            unit-triangularity.
306    
307            * DESCRIPTION (LicenseDetails): new; such that 'License:' becomes "canonical"
308    
309    2008-03-04  Martin Maechler  <maechler@stat.math.ethz.ch>
310    
311            * R/diagMatrix.R (subDiag): fix when x[..] became a vector
312    
313            * src/Tsparse.c (Tsparse_diagU2N): new utility, necessary for e.g.
314            * src/Csparse.c (Csparse_crossprod): use [CT]sparse_diagU2N() !!
315    
316            * R/Auxiliaries.R (.diagU2N): make use of new Tsparse_diagU2N
317    
318            * R/Ops.R ("-" (<sparseMatrix>)): use diagU2N()
319    
320            * src/chm_common.c (AS_CHM_FINISH): add note about problem
321            for triangular (diag = "U").
322    
323    2008-02-21  Martin Maechler  <maechler@stat.math.ethz.ch>
324    
325            * R/Auxiliaries.R (as_Csparse2): drop this, replacing by
326            * R/bind.R:  .Call(dense_to_Csparse, *)
327    
328    2008-02-20  Martin Maechler  <maechler@stat.math.ethz.ch>
329    
330            * R/Matrix.R (Matrix): no longer use coercions to specific classes
331                    (since we are discouraging them in user code).
332    
333            * tests/*.R: also replaces coercions to specific classes by
334            coercions to super classes.
335    
336            * R/denseMatrix.R (.dense2C): simplified by using forceSymmetric()
337    
338    
339    2008-02-19  Martin Maechler  <maechler@stat.math.ethz.ch>
340    
341            * man/CAex.Rd: example: coerce to symmetric*, not dsC*
342    
343            * src/dense.c (dense_band): generalized from ddense_band
344    
345            * R/ddenseMatrix.R (.trilDense,.triuDense, .bandDense):
346              now for "denseMatrix" (instead of just "ddense*"); much
347              simplified setMethod()s for these.
348    
349            * src/dense.c (dense_to_symmetric): generalized from ddense_*
350    
351    2008-02-18  Martin Maechler  <maechler@stat.math.ethz.ch>
352    
353            * R/AllGeneric.R: forceSymmetric() generic: fast no-checking
354            version of as(*, "symmetricMatric").
355    
356            * src/dense.c (ddense_to_symmetric): add 'symm_test' argument, and
357            * R/symmetricMatrix.R: set it TRUE in coercion to "symmetricMatrix"
358    
359    2008-02-16  Martin Maechler  <maechler@stat.math.ethz.ch>
360    
361            * R/Matrix.R (subset.ij): utility, as first step to faster
362               M [ <ij-matrix> ] indexing.
363    
364            * R/Matrix.R (.M.sub.i.logical): M[ <logical> ] : try better.
365    
366            * src/dense.c (ddense_symmpart, ddense_skewpart): new functions
367            for more efficient symmpart() and skewpart() methods.
368    
369            * src/Mutils.c (equal_string_vectors): utility
370    
371            * src/dense.c (ddense_to_symmetric): new function used in
372    
373            * R/symmetricMatrix.R: setAs(., "symmetricMatrix")
374    
375            * R/sparseMatrix.R, et_al (isSymmetric): add '...' to formals, in
376            order to match the generic (and evade .local(..)).
377    
378            * R/dsCMatrix.R: dgC -> dsC: use C code!
379    
380            * NAMESPACE, R/AllGeneric.R (symmpart, skewpart): new functions
381            as per TODO
382    
383            * R/Auxiliaries.R (setZero, all0Matrix): new utilities
384    
385            * R/symmetricMatrix.R: obvious symmpart(), skewpart() methods
386    
387    
388    2008-02-15  Martin Maechler  <maechler@stat.math.ethz.ch>
389    
390            * R/Ops.R (.Arith.Csparse): use diagU2N when needed in triangular
391    
392            * R/Auxiliaries.R (non0.i): take out of non0ind
393    
394            * R/ddenseMatrix.R (.trilDense, .triuDense, .bandDense):
395            make tril(), triu(), band() work for "matrix" and all "dense*"
396    
397            * R/triangularMatrix.R (.tri[lu].tr): need .diagU2N(*)
398            * tests/simple.R: test the fix above
399    
400            * R/sparseMatrix.R ([): simplification: no coerce to <general>
401                    before we use as(., <Tsparse>)[...] anyway
402    
403            * R/Rsparse.R (.viaC.to.R): mostly instead of .viaC.to.dgR()
404    
405            * R/triangularMatrix.R (isTriangular): methods for all subclasses
406            instead of "triangularMatrix" -- just to disambiguate
407    
408    2008-02-14  Martin Maechler  <maechler@stat.math.ethz.ch>
409    
410            * tests/Class+Meth.R (dotestMat): add m[FALSE, FALSE] { <-> TODO}
411            * tests/indexing.R: example that fails above
412    
413    2008-01-26  Martin Maechler  <maechler@stat.math.ethz.ch>
414    
415            * R/Matrix.R (.M.sub.i.2col): fix for logical matrix indexing
416            * R/Tsparse.R (.TM.sub.i.2col, .TM.repl.i.2col): ditto;
417                    now, M[lower.tri(M)] and  M[lower.tri(M)] <- v  work better
418    
419            * src/Tsparse.c (Tsparse_to_tCsparse): new fast utility.
420            * src/Tsparse.h, init.c: ditto
421            * R/Auxiliaries.R (isTriT): new; faster than going via Csparse
422                 both isTriC() and isTriT() now return TRUE with "kind" or FALSE.
423            * R/sparseMatrix.R (isTriangular): hence simplified
424    
425    2008-01-24  Martin Maechler  <maechler@stat.math.ethz.ch>
426    
427            * R/Ops.R (.Arith.Csparse): new utility factored out of former
428              <dgC> o <dgC>, extended for triangular and also used in  <dtC> o <dtC>.
429    
430    2008-01-23  Martin Maechler  <maechler@stat.math.ethz.ch>
431    
432            * tests/factorizing.R (checkSchur): and more tests for checking Schur()
433    
434            * inst/test-tools.R (isOrthogonal): new function; also file restructured
435    
436    2008-01-22  Martin Maechler  <maechler@stat.math.ethz.ch>
437    
438            * R/ngTMatrix.R: allow as(<numeric matrix>, "ngTMatrix") and hence
439            coercion to "nMatrix" and "pMatrix"
440    
441            * R/AllClass.R: "Schur" class;  "number" class union
442            * man/number-class.Rd:
443            * man/Schur-class.Rd:
444    
445            * R/eigen.R (.dgeSchur): utility, and return "Schur" class
446            (.simpleSchur): Schur() method for diagonal matrices
447            (.triSchur):    Schur() method for triangular matrices
448            (Schur.sym):    Schur() for symmetric matrices {building on eigen()}.
449    
450    
451    2008-01-21  Martin Maechler  <maechler@stat.math.ethz.ch>
452    
453            * src/dgCMatrix.c (dgCMatrix_QR): set @Dim slot (as per doc)
454    
455  2008-01-15  Martin Maechler  <maechler@stat.math.ethz.ch>  2008-01-15  Martin Maechler  <maechler@stat.math.ethz.ch>
456    
457          * R/CHMfactor.R (solve): method for b="numeric", but also b="ANY"          * R/CHMfactor.R (solve): method for b="numeric", but also b="ANY"

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