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revision 2159, Sat Mar 29 08:09:05 2008 UTC revision 2242, Thu Aug 21 20:51:40 2008 UTC
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1    2008-08-19  Martin Maechler  <maechler@stat.math.ethz.ch>
2    
3            * R/nsCMatrix.R (setAs(., dgTMatrix))): remove unused method
4    
5    2008-08-18  Martin Maechler  <maechler@stat.math.ethz.ch>
6    
7            * R/Ops.R (.Ops2dge.via.x, and many others): eliminate never-used
8            variable assignments {from "next version" codetools}.
9            * R/Csparse.R, R/Tsparse.R: ditto
10    
11    2008-08-17  Martin Maechler  <maechler@stat.math.ethz.ch>
12    
13            * R/sparseVector.R (sp2vec, coerce to sparseVector):
14            make sure no integer overflows happen, and use double precision
15            (n, index) where appropriate.
16    
17            * tests/Simple.R: test "large" sparse vectors.
18    
19    2008-08-14  Martin Maechler  <maechler@stat.math.ethz.ch>
20    
21            * R/AllClass.R (sparseVector): 'length' and 'i' are "numeric", not
22            just integer (allowing much longer length).
23    
24    2008-07-28  Martin Maechler  <maechler@stat.math.ethz.ch>
25    
26            * R/AllClass.R (diagonalMatrix): extend  "sparseMatrix" instead of
27            "denseMatrix".  This renders "scarceMatrix" dispensable and
28            invalidates part of MM's presentations on "space of Matrix
29            classes", but seems cleaner overall.
30    
31            * R/diagMatrix.R, etc: eliminate "scarceMatrix", replacing it by
32            "sparseMatrix" in method signatures;
33            further, instead of coercing to "sparseMatrix", coerce to
34            "TsparseMatrix" now.
35    
36    2008-07-26  Martin Maechler  <maechler@stat.math.ethz.ch>
37    
38            * src/dgCMatrix.c (dgCMatrix_qrsol): allow third argument 'order' in
39            .Call(.)
40            * R/sparseMatrix.R (lm.fit.sparse), src/dgCMatrix.h, src/init.c: ditto
41    
42    2008-07-24  Martin Maechler  <maechler@stat.math.ethz.ch>
43    
44            * R/dgeMatrix.R: need solve(<dge>, <sparse>) against infinite
45            recursion in new test in
46            * tests/matprod.R: testing the above and another solve() case, below
47    
48            * R/sparseMatrix.R (lm.fit.sparse): slightly more efficient for
49            e.g. triangular 'x'.
50    
51            * src/dgCMatrix.c (dgCMatrix_qrsol): use AS_CSP() hence allowing dtC*
52            * src/dgCMatrix.c (dgCMatrix_cholsol): use AS_CHM_SP() to work
53            correctly with unit-triangular x
54    
55            * src/dsCMatrix.c (dsCMatrix_Csparse_solve): use AS_CHM_SP()
56            instead of not checking diagU.
57    
58            * R/diagMatrix.R, R/Auxiliaries.R: tweaks to allow later
59            experiments where diagonalMatrix would extend sparse*.
60    
61    
62    2008-07-23  Martin Maechler  <maechler@stat.math.ethz.ch>
63    
64            * src/dgCMatrix.c (compressed_non_0_ij): for nnzero(), use
65            "x@p[ncol(x)]" instead of length(x@i).
66            * R/Auxiliaries.R (nnzero): ditto
67    
68            * src/chm_common.c (as_cholmod_sparse): Do not use LENGTH(islot)
69            since that fails for over-allocated i.
70    
71            * tests/validObj.R: more testing of over-allocated (i,x) slots
72    
73    2008-07-23  Martin Maechler  <maechler@stat.math.ethz.ch>
74    
75            * src/chm_common.c (as_cholmod_sparse): Add 4th argument
76            'sort_in_place' and set it to TRUE in call from
77            * src/Csparse.c (Csparse_validate): sort in place, making sure that
78            validObject() continues sort the columns if needed.
79    
80            * tests/validObj.R: now tests that more thoroughly, and
81            * man/CsparseMatrix-class.Rd: documents it.
82    
83    2008-07-21  Martin Maechler  <maechler@stat.math.ethz.ch>
84    
85            * src/cs_utils.c (Matrix_as_cs): add check_Udiag switch
86            * src/cs_utils.h (AS_CSP & AS_CSP__): two versions
87            * src/dtCMatrix.c (dtCMatrix_sparse_solve): no longer needs
88            diagU2N().
89    
90            * R/diagMatrix.R (.sparseDiagonal): new utility, used in "old"
91            .spDiagonal() and new .trDiagonal().
92    
93            * R/dtCMatrix.R (solve): make use of .trDiagonal()
94    
95    2008-07-19  Martin Maechler  <maechler@stat.math.ethz.ch>
96    
97            * R/Auxiliaries.R (dimNamesCheck): fix very long standing buglet,
98            stumbled upon by Michael H.
99    
100            * tests/validObj.R: testing the bug-fix
101    
102            * src/chm_common.h (AS_CHM_SP__, AS_CHM_TR__): the non-diagU2N
103            versions.
104    
105            * src/chm_common.c (as_cholmod_sparse, as_cholmod_triplet): new
106            boolean argument 'check_Udiag' (formerly implicitly was FALSE).
107    
108            * src/Csparse.c (Csparse_Csparse_prod, ...): etc: use the new
109              AS_CHM_SP() which includes diagU2N.
110    
111            * inst/include/Matrix_stubs.c (M_as_cholmod_sparse): similarly
112            adapt to 3 arguments.
113    
114    2008-07-17  Douglas Bates <bates@stat.wisc.edu>
115    
116            * [r2217] R/dtCMatrix.R, src/dtCMatrix.c, src/dtCMatrix.h, src/init.c:
117              Replace dtCMatrix_solve by more general dtCMatrix_sparse_solve and add
118              new solve method
119            * [r2216] src/cs_utils.c: Utility csp_eye in case we want to fold
120              Csparse_diagU2N functionality into Matrix_as_cs
121    
122    2008-07-17  Martin Maechler  <maechler@stat.math.ethz.ch>
123    
124            * inst/doc/factor2sparse.Rnw: revive a year-old unfinished vignette
125    
126    2008-07-16  Douglas Bates <bates@stat.wisc.edu>
127    
128            * [r2212] R/sparseMatrix.R: fac2sparse gets a drop.unused.levels
129              argument with default TRUE
130            * [r2211] inst/include/Matrix.h, inst/include/Matrix_stubs.c: Export
131              Csparse_diagU2N
132            * [r2210] R/dtCMatrix.R, man/dtCMatrix-class.Rd, src/dtCMatrix.c,
133              src/dtCMatrix.h, src/init.c: Remove vestigial methods based on the
134              parent array; new solve method for signature(a = "dtCMatrix", b =
135              "sparseMatrix")
136    
137    2008-07-14  Martin Maechler  <maechler@stat.math.ethz.ch>
138    
139            * R/diagMatrix.R (.bdiag): also keep result triangular
140    
141    2008-07-13  Douglas Bates <bates@stat.wisc.edu>
142    
143            * [r2208] src/dtCMatrix.c, src/dtTMatrix.c: Revise wording in error
144              messages
145    
146    2008-07-12  Martin Maechler  <maechler@stat.math.ethz.ch>
147    
148            * R/diagMatrix.R (.bdiag): make more sophisticated, keeping
149            symmetric- or nsparse-Matrix, also fixing the bug introduced with
150            the new version (.999375-10).
151    
152            * tests/Simple.R: regression test for the bugs.
153    
154    2008-07-07  Martin Maechler  <maechler@stat.math.ethz.ch>
155    
156            * R/sparseVector.R (spV2M): fix for "isparseVector".
157            Further, fix <diag> -> <sparseVector> coercion
158            (repSpV): add rep(<sparseVector>, .) method
159    
160            * R/sparseMatrix.R ([<-): when the RHS is a "scarce"Matrix, do *not*
161            use as.vector(.).
162    
163            * R/Tsparse.R ([<-): & [CR]sparse.R: methods for value = "sparseVector"
164    
165            * R/AllClass.R: new (hidden) class union "scarceMatrix"
166            * R/AllClass.R: sparseVector: add prototype
167    
168            * src/dsCMatrix.c (chk_nm): fix "Cholesky" check, thanks to
169            Kasper Kristensen
170    
171    2008-06-28  Martin Maechler  <maechler@stat.math.ethz.ch>
172    
173            * tests/other-pkgs.R: add more interesting Matrix -> graph
174    
175    2008-06-27  Martin Maechler  <maechler@stat.math.ethz.ch>
176    
177            * R/sparseMatrix.R (Tsp2grNEL): add 'need.uniq' argument for speed
178            improvement in "[CR]sparseMatrix" -> "graphNEL" coercion.
179    
180    2008-06-25  Martin Maechler  <maechler@stat.math.ethz.ch>
181    
182            * DESCRIPTION: release 0.999375-10 to CRAN
183    
184            * R/diagMatrix.R (.bdiag): use more efficient Bates-algorithm for
185            .bdiag().
186            * man/bdiag.Rd: update, including test.
187    
188    2008-06-24  Martin Maechler  <maechler@stat.math.ethz.ch>
189    
190            * tests/Simple.R: add minimal bdiag() checks
191    
192            * R/diagMatrix.R (bdiag): fix bdiag(diag(4:5)) case;
193              factor out the Tsparse - internal computation into new .bdiag()
194    
195    2008-06-14  Martin Maechler  <maechler@stat.math.ethz.ch>
196    
197            * R/nsparseMatrix.R: specific fast all() and any() methods.
198    
199            * src/dgTMatrix.c (MAKE_gTMatrix_to_geMatrix): better error message
200            when trying to produce too large result.
201    
202            * inst/test-tools.R (checkMatrix): add 'do.matrix' with a check for
203            very large matrices.
204    
205            * R/sparseMatrix.R (printSpMatrix2): new function, used by
206            show(<sparseMatrix>).
207    
208            * R/diagMatrix.R (show): print only diagonal entries when nrow(.) >= 50.
209    
210    2008-06-13  Martin Maechler  <maechler@stat.math.ethz.ch>
211    
212            * src/Mutils.c (m_encodeInd, m_encodeInd2):
213            * R/*.R: .Call(m_encodeInd2?, ..) instead of encodeInd2?(..).
214    
215            * R/Auxiliaries.R (encodeInd2?): care against integer overflow (for
216            big matrices): -> 2nd argument 'di' instead of 'nr' !
217    
218    2008-06-09  Martin Maechler  <maechler@stat.math.ethz.ch>
219    
220            * R/dtCMatrix.R: faster dgC* -> dtC* method
221            * tests/Simple.R: (hence removed "FIXME")
222    
223            * R/Auxiliaries.R (copyClass): add 'check = .copyClass.check'
224            which can be be turned off for possible speed gains.
225    
226    2008-06-02  Martin Maechler  <maechler@stat.math.ethz.ch>
227    
228            * R/dMatrix.R, R/Tsparse.R: get rid of some disambiguation warnings
229    
230            * R/not.R: fix !<ldiMatrix>
231            implement two old "FIXME"s:  !<ldenseMatrix> & !<ndenseMatrix>
232    
233            * R/diagMatrix.R (Ops): fix one-off thinko in
234            <diagonal> o <numeric> methods
235    
236            * inst/test-tools.R: checkMatrix(): drop0(m12) unconditionally
237    
238    2008-05-30  Martin Maechler  <maechler@stat.math.ethz.ch>
239    
240            * R/diagMatrix.R (Ops): more <diagonal> o <Matrix> methods
241            * tests/Simple.R: testing the above
242    
243    2008-05-07  Martin Maechler  <maechler@stat.math.ethz.ch>
244    
245            * NAMESPACE: also import "Ops" {found via new tools:::get_S4_generics_with_methods()}
246    
247    2008-05-03  Martin Maechler  <maechler@stat.math.ethz.ch>
248    
249            * R/Matrix.R (dimnames<-): dimnames(.) <- NULL works with a message;
250            * NAMESPACE (unname): finally exported
251    
252    2008-04-28  Martin Maechler  <maechler@stat.math.ethz.ch>
253    
254            * R/Auxiliaries.R (cholMat): possibly keep packed
255    
256            * inst/test-tools.R (checkMatrix): add fixed determinant.matrix()
257            for R < 2.7.0.
258    
259            * R/Tsparse.R ([): for triangularMatrix, check if result may be
260            triangular.
261            * tests/indexing.R: regression test
262    
263    2008-04-26  Martin Maechler  <maechler@stat.math.ethz.ch>
264    
265            * inst/test-tools.R (checkMatrix): test <Ops> not only for dMatrix
266            * R/Ops.R: more methods, for lMatrix/nMatrix
267    
268    2008-04-24  Martin Maechler  <maechler@stat.math.ethz.ch>
269    
270            * R/expm.R: new file for all expm() methods; notably new ones for
271            diagonal*, triangular*, symmetric* and also simple "matrix".
272    
273    2008-04-23  Martin Maechler  <maechler@stat.math.ethz.ch>
274    
275            * R/dsyMatrix.R: setAs(.) rather than setIs(.)  "to dpoMatrix"
276    
277            * inst/test-tools.R (assert.EQ.mat): better message when not equal
278    
279            * src/dgeMatrix.c (dgeMatrix_matrix_crossprod): allow integer RHS.
280    
281            * R/AllClass.R (ddiMatrix,ldiMatrix): extend [dl]Matrix instead of
282            [dl]denseMatrix {identical slots; but more logical method dispatch}
283    
284    2008-04-23  Martin Maechler  <maechler@stat.math.ethz.ch>
285    
286            * R/sparseMatrix.R (summary): use length(<i-slot>) instead of nnzero()
287    
288            * R/diagMatrix.R (determinant): method
289    
290    2008-04-22  Martin Maechler  <maechler@stat.math.ethz.ch>
291    
292            * src/dsCMatrix.c (dsCMatrix_Cholesky): suppress CHOLMOD printing too
293    
294            * R/Rsparse.R (.viaC.to.R): uplo fix for symmetric & triangular
295    
296            * R/dsCMatrix.R (determinant): switch to use Cholesky( 'LDL' ) and
297            its diagonal
298    
299    2008-04-21  Martin Maechler  <maechler@stat.math.ethz.ch>
300    
301            * R/dMatrix.R (Summary): short-cut for prod(<sparse>)
302    
303            * R/not.R: fix !<"U"-diag-ltrMatrix> ; drop {R < 2.6.0}-branch
304    
305            * R/Auxiliaries.R (tT2gT): fix for "U"-diag-ltTMatrix
306    
307            * R/AllClass.R: ltTMatrix validity: call (more stringent) tTMatrix_validate
308    
309    2008-04-19  Martin Maechler  <maechler@stat.math.ethz.ch>
310    
311            * R/Ops.R (Ops.x.x): aux.function, not just for (dMatrix,dMatrix)
312    
313            * R/Ops.R (.do.Logic.lsparse): fix NA case
314    
315            * R/Tsparse.R (replTmat): fix r.sym case, using indTri()
316    
317            * R/Auxiliaries.R (nnzero): fix special cases, using
318            * R/Auxiliaries.R (indDiag): new utility
319            * R/Auxiliaries.R (indTri): new argument 'diag'
320    
321            * R/dMatrix.R: Summmary(<ddenseMatrix>): different branch for dsy*
322    
323    2008-04-18  Martin Maechler  <maechler@stat.math.ethz.ch>
324    
325            * R/diagMatrix.R: "Summary" methods, and more "Arith" / "Ops"
326    
327            * src/Csparse.c (Csparse_drop): preserve (uplo,diag) for
328            ".tCMatrix" triangular matrix.
329    
330            * R/Auxiliaries.R (drop0): use diagU2N(); according to helpfile,
331            'clx' can be class *or* class representation.
332            (nnzSparse): new.
333            (non0ind): new 'xtendSymm' argument; used in
334            * R/Ops.R:
335    
336            * R/pMatrix.R: more efficient determinant() method
337    
338    2008-04-17  Martin Maechler  <maechler@stat.math.ethz.ch>
339    
340            * [disactivated] R/Matrix.R (det): det() as base::det(), but with Matrix environment
341            * [disactivated] NAMESPACE: export(det)
342    
343            * R/diagMatrix.R (mkDiag): new substitute for diag()
344    
345            * R/Auxiliaries.R (nnzero): fix for "diagU2N"-case
346            (as0, as1): new utility.
347    
348            * R/Csparse.R (diag, band): need diagU2N()
349    
350            * src/dgeMatrix.c (get_norm): return NA when 'x' slot has NA/NaN.
351    
352            * R/lMatrix.R: coerce(nMatrix |-> lMatrix) fix
353    
354            * R/Ops.R (Compare): fix <nsp> o <nsp> case
355    
356            * R/nsparseMatrix.R, R/pMatrix.R: is.na() method
357    
358    2008-04-16  Martin Maechler  <maechler@stat.math.ethz.ch>
359    
360            * R/Auxiliaries.R (signPerm): new utility for
361            * R/Auxiliaries.R (detSparseLU): determinant() via sparseLU
362    
363            * src/dsCMatrix.c (dsCMatrix_LDL_D): suppress 'CHOLMOD warning';
364            since we have our own error handler (and can use tryCatch() from R).
365    
366    2008-04-15  Martin Maechler  <maechler@stat.math.ethz.ch>
367    
368            * R/dgTMatrix.R (image): ha! set col=NA if lwd is small -- very nice!
369    
370            * R/dsCMatrix.R (determinant): use tryCatch() and switch to lu()
371            when not positive definite.
372    
373            * R/Auxiliaries.R (asTri): new auxiliary
374            (non0.i): make *much* faster for Tsparse with many non-zero
375            entries; add 'uniqT = TRUE' argument to be used when sorting is undesired.
376    
377            * tests/Class+Meth.R (dotestMat): now build on checkMatrix() from
378            test-tools.R , see below
379    
380            * R/dMatrix.R: fix "Summary" method: + diagU2N()
381    
382            * NAMESPACE, R/Matrix.R: add mean() method
383    
384    2008-04-12  Martin Maechler  <maechler@stat.math.ethz.ch>
385    
386            * R/dgTMatrix.R (image): allow to *not* take abs(), and use
387            cold-hot colors; try *changed* default useAbs = FALSE
388            * man/image-methods.Rd:  nice examples
389    
390    2008-04-11  Martin Maechler  <maechler@stat.math.ethz.ch>
391    
392            * inst/test-tools.R (checkMatrix): new function for modularizing part
393            of tstMatrixClass() in tests/Class+Meth.R
394    
395            * R/dsCMatrix.R: coercion from "matrix"
396            * R/ltTMatrix.R, R/ntTMatrix.R: ditto (change it).
397    
398            * tests/Class+Meth.R (tstMatrixClass): some cleanup;
399            add test for as(matrix(,0,0), <class>)
400    
401    2008-04-09  Martin Maechler  <maechler@stat.math.ethz.ch>
402    
403            * src/dgeMatrix.c (dgeMatrix_determinant): for n == 0,
404            work as determinant(matrix(,0,0)).
405    
406            * src/dgCMatrix.c (dgCMatrix_LU): return {L,U} as dtCMatrix
407            * man/sparseLU-class.Rd: ditto
408    
409            * R/dgCMatrix.R (determinant): method building on lu()
410            * R/sparseMatrix.R, Matrix.R, ...: ditto
411    
412            * R/Auxiliaries.R (mkDet): auxiliary for determinant()
413    
414    2008-04-07  Martin Maechler  <maechler@stat.math.ethz.ch>
415    
416            * R/sparseMatrix.R (summary<sparseMatrix>): no 'x' column for
417            pattern matrices.
418    
419    2008-04-02  Martin Maechler  <maechler@stat.math.ethz.ch>
420    
421            * src/dense.c (dense_to_Csparse): all declarations *before*
422            R_CheckStack(); needed e.g. for ancient gcc 2.96.
423    
424    
425  2008-03-29  Martin Maechler  <maechler@stat.math.ethz.ch>  2008-03-29  Martin Maechler  <maechler@stat.math.ethz.ch>
426    
427          * DESCRIPTION (Version): 0.999375-9 --- need to release          * DESCRIPTION (Version): 0.999375-9 --- need to release
428          for R-devel (and R 2.7.0 alpha soon).          for R-devel (and R 2.7.0 alpha soon).
429    
430            * R/AllClass.R: drop "double" from "atomicVector" class union
431    
432            * R/AllGeneric.R (rcond): check for base::rcond instead of R version
433            * R/dgeMatrix.R: ditto
434    
435          * R/sparseMatrix.R (summary): count NAs          * R/sparseMatrix.R (summary): count NAs
436    
437            * inst/doc/Intro2Matrix.Rnw: changes, aim for *one* introduction.
438    
439  2008-03-28  Martin Maechler  <maechler@stat.math.ethz.ch>  2008-03-28  Martin Maechler  <maechler@stat.math.ethz.ch>
440    
441          * R/AllGeneric.R: rcond(., norm) instead of rcond(., type), in          * R/AllGeneric.R: rcond(., norm) instead of rcond(., type), in

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