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revision 2105, Tue Jan 15 10:16:29 2008 UTC revision 2196, Fri May 30 21:49:50 2008 UTC
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1    2008-05-30  Martin Maechler  <maechler@stat.math.ethz.ch>
2    
3            * R/diagMatrix.R (Ops): more <diagonal> o <Matrix> methods
4            * tests/Simple.R: testing the above
5    
6    2008-05-07  Martin Maechler  <maechler@stat.math.ethz.ch>
7    
8            * NAMESPACE: also import "Ops" {found via new tools:::get_S4_generics_with_methods()}
9    
10    2008-05-03  Martin Maechler  <maechler@stat.math.ethz.ch>
11    
12            * R/Matrix.R (dimnames<-): dimnames(.) <- NULL works with a message;
13            * NAMESPACE (unname): finally exported
14    
15    2008-04-28  Martin Maechler  <maechler@stat.math.ethz.ch>
16    
17            * R/Auxiliaries.R (cholMat): possibly keep packed
18    
19            * inst/test-tools.R (checkMatrix): add fixed determinant.matrix()
20            for R < 2.7.0.
21    
22            * R/Tsparse.R ([): for triangularMatrix, check if result may be
23            triangular.
24            * tests/indexing.R: regression test
25    
26    2008-04-26  Martin Maechler  <maechler@stat.math.ethz.ch>
27    
28            * inst/test-tools.R (checkMatrix): test <Ops> not only for dMatrix
29            * R/Ops.R: more methods, for lMatrix/nMatrix
30    
31    2008-04-24  Martin Maechler  <maechler@stat.math.ethz.ch>
32    
33            * R/expm.R: new file for all expm() methods; notably new ones for
34            diagonal*, triangular*, symmetric* and also simple "matrix".
35    
36    2008-04-23  Martin Maechler  <maechler@stat.math.ethz.ch>
37    
38            * R/dsyMatrix.R: setAs(.) rather than setIs(.)  "to dpoMatrix"
39    
40            * inst/test-tools.R (assert.EQ.mat): better message when not equal
41    
42            * src/dgeMatrix.c (dgeMatrix_matrix_crossprod): allow integer RHS.
43    
44            * R/AllClass.R (ddiMatrix,ldiMatrix): extend [dl]Matrix instead of
45            [dl]denseMatrix {identical slots; but more logical method dispatch}
46    
47    2008-04-23  Martin Maechler  <maechler@stat.math.ethz.ch>
48    
49            * R/sparseMatrix.R (summary): use length(<i-slot>) instead of nnzero()
50    
51            * R/diagMatrix.R (determinant): method
52    
53    2008-04-22  Martin Maechler  <maechler@stat.math.ethz.ch>
54    
55            * src/dsCMatrix.c (dsCMatrix_Cholesky): suppress CHOLMOD printing too
56    
57            * R/Rsparse.R (.viaC.to.R): uplo fix for symmetric & triangular
58    
59            * R/dsCMatrix.R (determinant): switch to use Cholesky( 'LDL' ) and
60            its diagonal
61    
62    2008-04-21  Martin Maechler  <maechler@stat.math.ethz.ch>
63    
64            * R/dMatrix.R (Summary): short-cut for prod(<sparse>)
65    
66            * R/not.R: fix !<"U"-diag-ltrMatrix> ; drop {R < 2.6.0}-branch
67    
68            * R/Auxiliaries.R (tT2gT): fix for "U"-diag-ltTMatrix
69    
70            * R/AllClass.R: ltTMatrix validity: call (more stringent) tTMatrix_validate
71    
72    2008-04-19  Martin Maechler  <maechler@stat.math.ethz.ch>
73    
74            * R/Ops.R (Ops.x.x): aux.function, not just for (dMatrix,dMatrix)
75    
76            * R/Ops.R (.do.Logic.lsparse): fix NA case
77    
78            * R/Tsparse.R (replTmat): fix r.sym case, using indTri()
79    
80            * R/Auxiliaries.R (nnzero): fix special cases, using
81            * R/Auxiliaries.R (indDiag): new utility
82            * R/Auxiliaries.R (indTri): new argument 'diag'
83    
84            * R/dMatrix.R: Summmary(<ddenseMatrix>): different branch for dsy*
85    
86    2008-04-18  Martin Maechler  <maechler@stat.math.ethz.ch>
87    
88            * R/diagMatrix.R: "Summary" methods, and more "Arith" / "Ops"
89    
90            * src/Csparse.c (Csparse_drop): preserve (uplo,diag) for
91            ".tCMatrix" triangular matrix.
92    
93            * R/Auxiliaries.R (drop0): use diagU2N(); according to helpfile,
94            'clx' can be class *or* class representation.
95            (nnzSparse): new.
96            (non0ind): new 'xtendSymm' argument; used in
97            * R/Ops.R:
98    
99            * R/pMatrix.R: more efficient determinant() method
100    
101    2008-04-17  Martin Maechler  <maechler@stat.math.ethz.ch>
102    
103            * [disactivated] R/Matrix.R (det): det() as base::det(), but with Matrix environment
104            * [disactivated] NAMESPACE: export(det)
105    
106            * R/diagMatrix.R (mkDiag): new substitute for diag()
107    
108            * R/Auxiliaries.R (nnzero): fix for "diagU2N"-case
109            (as0, as1): new utility.
110    
111            * R/Csparse.R (diag, band): need diagU2N()
112    
113            * src/dgeMatrix.c (get_norm): return NA when 'x' slot has NA/NaN.
114    
115            * R/lMatrix.R: coerce(nMatrix |-> lMatrix) fix
116    
117            * R/Ops.R (Compare): fix <nsp> o <nsp> case
118    
119            * R/nsparseMatrix.R, R/pMatrix.R: is.na() method
120    
121    2008-04-16  Martin Maechler  <maechler@stat.math.ethz.ch>
122    
123            * R/Auxiliaries.R (signPerm): new utility for
124            * R/Auxiliaries.R (detSparseLU): determinant() via sparseLU
125    
126            * src/dsCMatrix.c (dsCMatrix_LDL_D): suppress 'CHOLMOD warning';
127            since we have our own error handler (and can use tryCatch() from R).
128    
129    2008-04-15  Martin Maechler  <maechler@stat.math.ethz.ch>
130    
131            * R/dgTMatrix.R (image): ha! set col=NA if lwd is small -- very nice!
132    
133            * R/dsCMatrix.R (determinant): use tryCatch() and switch to lu()
134            when not positive definite.
135    
136            * R/Auxiliaries.R (asTri): new auxiliary
137            (non0.i): make *much* faster for Tsparse with many non-zero
138            entries; add 'uniqT = TRUE' argument to be used when sorting is undesired.
139    
140            * tests/Class+Meth.R (dotestMat): now build on checkMatrix() from
141            test-tools.R , see below
142    
143            * R/dMatrix.R: fix "Summary" method: + diagU2N()
144    
145            * NAMESPACE, R/Matrix.R: add mean() method
146    
147    2008-04-12  Martin Maechler  <maechler@stat.math.ethz.ch>
148    
149            * R/dgTMatrix.R (image): allow to *not* take abs(), and use
150            cold-hot colors; try *changed* default useAbs = FALSE
151            * man/image-methods.Rd:  nice examples
152    
153    2008-04-11  Martin Maechler  <maechler@stat.math.ethz.ch>
154    
155            * inst/test-tools.R (checkMatrix): new function for modularizing part
156            of tstMatrixClass() in tests/Class+Meth.R
157    
158            * R/dsCMatrix.R: coercion from "matrix"
159            * R/ltTMatrix.R, R/ntTMatrix.R: ditto (change it).
160    
161            * tests/Class+Meth.R (tstMatrixClass): some cleanup;
162            add test for as(matrix(,0,0), <class>)
163    
164    2008-04-09  Martin Maechler  <maechler@stat.math.ethz.ch>
165    
166            * src/dgeMatrix.c (dgeMatrix_determinant): for n == 0,
167            work as determinant(matrix(,0,0)).
168    
169            * src/dgCMatrix.c (dgCMatrix_LU): return {L,U} as dtCMatrix
170            * man/sparseLU-class.Rd: ditto
171    
172            * R/dgCMatrix.R (determinant): method building on lu()
173            * R/sparseMatrix.R, Matrix.R, ...: ditto
174    
175            * R/Auxiliaries.R (mkDet): auxiliary for determinant()
176    
177    2008-04-07  Martin Maechler  <maechler@stat.math.ethz.ch>
178    
179            * R/sparseMatrix.R (summary<sparseMatrix>): no 'x' column for
180            pattern matrices.
181    
182    2008-04-02  Martin Maechler  <maechler@stat.math.ethz.ch>
183    
184            * src/dense.c (dense_to_Csparse): all declarations *before*
185            R_CheckStack(); needed e.g. for ancient gcc 2.96.
186    
187    
188    2008-03-29  Martin Maechler  <maechler@stat.math.ethz.ch>
189    
190            * DESCRIPTION (Version): 0.999375-9 --- need to release
191            for R-devel (and R 2.7.0 alpha soon).
192    
193            * R/AllClass.R: drop "double" from "atomicVector" class union
194    
195            * R/AllGeneric.R (rcond): check for base::rcond instead of R version
196            * R/dgeMatrix.R: ditto
197    
198            * R/sparseMatrix.R (summary): count NAs
199    
200            * inst/doc/Intro2Matrix.Rnw: changes, aim for *one* introduction.
201    
202    2008-03-28  Martin Maechler  <maechler@stat.math.ethz.ch>
203    
204            * R/AllGeneric.R: rcond(., norm) instead of rcond(., type), in
205            order to become compatible to new R 2.7.0 base::rcond().
206    
207    2008-03-25  Martin Maechler  <maechler@stat.math.ethz.ch>
208    
209            * DESCRIPTION (Version,Date): 0.999375-8 --- released to CRAN
210    
211            * R/diagMatrix.R (Ops): fix newly introduce bug in <.di> o <numeric>
212    
213            * inst/test-tools.R (isValid): new utility, used much in
214            * tests/simple.R:
215    
216            * man/BunchKaufman-methods.Rd: added too
217    
218    2008-03-24  Martin Maechler  <maechler@stat.math.ethz.ch>
219    
220            * R/dsyMatrix.R: add BunchKaufman() methods.
221            * R/dspMatrix.R:
222    
223            * src/init.c: add dsyMatrix_trf
224    
225    2008-03-23  Douglas Bates <bates@stat.wisc.edu>
226    
227            * DESCRIPTION (Version): release 0.999375-7
228            * src/CHMfactor.c (CHMfactor_update): fix
229    
230    2008-03-22  Martin Maechler  <maechler@stat.math.ethz.ch>
231    
232            * src/dsCMatrix.c (dsCMatrix_LDL_D): cleanup, also using
233            internal_chm_factor().
234    
235            * R/AllGeneric.R: do *not* define a "chol" generic
236                    (but rather use the implicit one *without* making pivot
237                    part of the signature)
238            * R/*.R: drop the 'pivot' from chol's signature and make
239                    'pivot=FALSE' a default argument of method definitions.
240    
241            * .Rbuildignore: add 'wrld_1deg': I.e. do not put it into released
242            version of Matrix
243    
244    2008-03-18  Martin Maechler  <maechler@stat.math.ethz.ch>
245    
246            * R/Tsparse.R (.T.2.n): drop 0's before coercion to "nMatrix"
247    
248            * R/sparseMatrix.R (is.na): new simple method
249            * R/denseMatrix.R (is.na): ditto.
250    
251            * R/diagMatrix.R (.symDiagonal): newly exported utility.
252    
253            * R/diagMatrix.R (Ops): <diag> * <numeric> should not become dgeMatrix!
254    
255            * src/UFsparse_download.sh: -->
256            * src/CHOLMOD/: update to CHOLMOD version 1.6 (Nov.2007)
257    
258    2008-03-17  Martin Maechler  <maechler@stat.math.ethz.ch>
259    
260            * src/dsCMatrix.c (dsCMatrix_LDL_D): even faster utility with same
261            functionality; barely tested in
262            * tests/factorizing.R
263    
264            * src/Csparse.c (diag_tC): new functionality to enable faster
265            determinant(<dsCMatrix>, .) in
266            * R/dsCMatrix.R
267    
268    2008-03-17 18:53  Douglas Bates <bates@stat.wisc.edu>
269    
270            * R/CHMfactor.R, inst/include/Matrix.h, inst/include/Matrix_stubs.c,
271              src/CHMfactor.c, src/CHMfactor.h,
272              man/CHMfactor-class.Rd, src/init.c, tests/factorizing.R:
273              Log-determinant of the parent matrix from a CHMfactor object as
274              chm_factor_ldetL2; documentation and support
275    
276    2008-03-15  Martin Maechler  <maechler@stat.math.ethz.ch>
277    
278            * R/dsCMatrix.R: enable determinant(<dsCMatrix>, .) via chol(.)
279    
280    2008-03-14  Martin Maechler  <maechler@stat.math.ethz.ch>
281    
282            * R/dsCMatrix.R: setAs(., "dsCMatrix") but with a deprecation
283            warning.
284    
285    2008-03-13  Martin Maechler  <maechler@stat.math.ethz.ch>
286    
287            * DESCRIPTION (Version, Date): bug-fix release 0.999375-6
288    
289            * R/diagMatrix.R (diag2tT.u): utility to be smarter in
290              <diagonal> o <sparse_triangular>
291              setAs(., "nMatrix") added.
292    
293            * R/diagMatrix.R (Diagonal): Diagonal(4, x=3) now works too
294    
295            * R/Auxiliaries.R (.diagU2N): more careful coercion in 2 steps
296                    new argument 'checkDense = FALSE'.
297    
298    
299    2008-03-07  Martin Maechler  <maechler@stat.math.ethz.ch>
300    
301            * src/dgeMatrix.c (dgeMatrix_exp): fix the octave-origin bug in the
302            back-permutation of the matrix exponential.
303    
304            * tests/matr-exp.R: test the fix (for an example where expm() was wrong).
305    
306            * DESCRIPTION (Date,Version): ready to release 0.999375-5
307    
308            * tests/simple.R: testing diagN2U
309    
310    2008-03-06  Martin Maechler  <maechler@stat.math.ethz.ch>
311    
312            * R/Auxiliaries.R (diagN2U): interface to
313    
314            * src/Csparse.c (Csparse_diagN2U): .Call()able SEXP version of chm_diagN2U()
315    
316            * tests/matprod.R: test for triangularity preserving <dtC> %*% <dtC>
317    
318    2008-03-05  Martin Maechler  <maechler@stat.math.ethz.ch>
319    
320            * src/chm_common.c (chm_diagN2U): new utility.
321    
322            * src/Csparse.c (Csparse_Csparse_crossprod, Csparse_Csparse_prod):
323            make use of chm_diagN2U() and hence now preserve triangularity and
324            unit-triangularity.
325    
326            * DESCRIPTION (LicenseDetails): new; such that 'License:' becomes "canonical"
327    
328    2008-03-04  Martin Maechler  <maechler@stat.math.ethz.ch>
329    
330            * R/diagMatrix.R (subDiag): fix when x[..] became a vector
331    
332            * src/Tsparse.c (Tsparse_diagU2N): new utility, necessary for e.g.
333            * src/Csparse.c (Csparse_crossprod): use [CT]sparse_diagU2N() !!
334    
335            * R/Auxiliaries.R (.diagU2N): make use of new Tsparse_diagU2N
336    
337            * R/Ops.R ("-" (<sparseMatrix>)): use diagU2N()
338    
339            * src/chm_common.c (AS_CHM_FINISH): add note about problem
340            for triangular (diag = "U").
341    
342    2008-02-21  Martin Maechler  <maechler@stat.math.ethz.ch>
343    
344            * R/Auxiliaries.R (as_Csparse2): drop this, replacing by
345            * R/bind.R:  .Call(dense_to_Csparse, *)
346    
347    2008-02-20  Martin Maechler  <maechler@stat.math.ethz.ch>
348    
349            * R/Matrix.R (Matrix): no longer use coercions to specific classes
350                    (since we are discouraging them in user code).
351    
352            * tests/*.R: also replaces coercions to specific classes by
353            coercions to super classes.
354    
355            * R/denseMatrix.R (.dense2C): simplified by using forceSymmetric()
356    
357    
358    2008-02-19  Martin Maechler  <maechler@stat.math.ethz.ch>
359    
360            * man/CAex.Rd: example: coerce to symmetric*, not dsC*
361    
362            * src/dense.c (dense_band): generalized from ddense_band
363    
364            * R/ddenseMatrix.R (.trilDense,.triuDense, .bandDense):
365              now for "denseMatrix" (instead of just "ddense*"); much
366              simplified setMethod()s for these.
367    
368            * src/dense.c (dense_to_symmetric): generalized from ddense_*
369    
370    2008-02-18  Martin Maechler  <maechler@stat.math.ethz.ch>
371    
372            * R/AllGeneric.R: forceSymmetric() generic: fast no-checking
373            version of as(*, "symmetricMatric").
374    
375            * src/dense.c (ddense_to_symmetric): add 'symm_test' argument, and
376            * R/symmetricMatrix.R: set it TRUE in coercion to "symmetricMatrix"
377    
378    2008-02-16  Martin Maechler  <maechler@stat.math.ethz.ch>
379    
380            * R/Matrix.R (subset.ij): utility, as first step to faster
381               M [ <ij-matrix> ] indexing.
382    
383            * R/Matrix.R (.M.sub.i.logical): M[ <logical> ] : try better.
384    
385            * src/dense.c (ddense_symmpart, ddense_skewpart): new functions
386            for more efficient symmpart() and skewpart() methods.
387    
388            * src/Mutils.c (equal_string_vectors): utility
389    
390            * src/dense.c (ddense_to_symmetric): new function used in
391    
392            * R/symmetricMatrix.R: setAs(., "symmetricMatrix")
393    
394            * R/sparseMatrix.R, et_al (isSymmetric): add '...' to formals, in
395            order to match the generic (and evade .local(..)).
396    
397            * R/dsCMatrix.R: dgC -> dsC: use C code!
398    
399            * NAMESPACE, R/AllGeneric.R (symmpart, skewpart): new functions
400            as per TODO
401    
402            * R/Auxiliaries.R (setZero, all0Matrix): new utilities
403    
404            * R/symmetricMatrix.R: obvious symmpart(), skewpart() methods
405    
406    
407    2008-02-15  Martin Maechler  <maechler@stat.math.ethz.ch>
408    
409            * R/Ops.R (.Arith.Csparse): use diagU2N when needed in triangular
410    
411            * R/Auxiliaries.R (non0.i): take out of non0ind
412    
413            * R/ddenseMatrix.R (.trilDense, .triuDense, .bandDense):
414            make tril(), triu(), band() work for "matrix" and all "dense*"
415    
416            * R/triangularMatrix.R (.tri[lu].tr): need .diagU2N(*)
417            * tests/simple.R: test the fix above
418    
419            * R/sparseMatrix.R ([): simplification: no coerce to <general>
420                    before we use as(., <Tsparse>)[...] anyway
421    
422            * R/Rsparse.R (.viaC.to.R): mostly instead of .viaC.to.dgR()
423    
424            * R/triangularMatrix.R (isTriangular): methods for all subclasses
425            instead of "triangularMatrix" -- just to disambiguate
426    
427    2008-02-14  Martin Maechler  <maechler@stat.math.ethz.ch>
428    
429            * tests/Class+Meth.R (dotestMat): add m[FALSE, FALSE] { <-> TODO}
430            * tests/indexing.R: example that fails above
431    
432    2008-01-26  Martin Maechler  <maechler@stat.math.ethz.ch>
433    
434            * R/Matrix.R (.M.sub.i.2col): fix for logical matrix indexing
435            * R/Tsparse.R (.TM.sub.i.2col, .TM.repl.i.2col): ditto;
436                    now, M[lower.tri(M)] and  M[lower.tri(M)] <- v  work better
437    
438            * src/Tsparse.c (Tsparse_to_tCsparse): new fast utility.
439            * src/Tsparse.h, init.c: ditto
440            * R/Auxiliaries.R (isTriT): new; faster than going via Csparse
441                 both isTriC() and isTriT() now return TRUE with "kind" or FALSE.
442            * R/sparseMatrix.R (isTriangular): hence simplified
443    
444    2008-01-24  Martin Maechler  <maechler@stat.math.ethz.ch>
445    
446            * R/Ops.R (.Arith.Csparse): new utility factored out of former
447              <dgC> o <dgC>, extended for triangular and also used in  <dtC> o <dtC>.
448    
449    2008-01-23  Martin Maechler  <maechler@stat.math.ethz.ch>
450    
451            * tests/factorizing.R (checkSchur): and more tests for checking Schur()
452    
453            * inst/test-tools.R (isOrthogonal): new function; also file restructured
454    
455    2008-01-22  Martin Maechler  <maechler@stat.math.ethz.ch>
456    
457            * R/ngTMatrix.R: allow as(<numeric matrix>, "ngTMatrix") and hence
458            coercion to "nMatrix" and "pMatrix"
459    
460            * R/AllClass.R: "Schur" class;  "number" class union
461            * man/number-class.Rd:
462            * man/Schur-class.Rd:
463    
464            * R/eigen.R (.dgeSchur): utility, and return "Schur" class
465            (.simpleSchur): Schur() method for diagonal matrices
466            (.triSchur):    Schur() method for triangular matrices
467            (Schur.sym):    Schur() for symmetric matrices {building on eigen()}.
468    
469    
470    2008-01-21  Martin Maechler  <maechler@stat.math.ethz.ch>
471    
472            * src/dgCMatrix.c (dgCMatrix_QR): set @Dim slot (as per doc)
473    
474  2008-01-15  Martin Maechler  <maechler@stat.math.ethz.ch>  2008-01-15  Martin Maechler  <maechler@stat.math.ethz.ch>
475    
476          * 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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