SCM

SCM Repository

[matrix] Diff of /pkg/ChangeLog
ViewVC logotype

Diff of /pkg/ChangeLog

Parent Directory Parent Directory | Revision Log Revision Log | View Patch Patch

revision 2159, Sat Mar 29 08:09:05 2008 UTC revision 2247, Mon Aug 25 16:56:00 2008 UTC
# Line 1  Line 1 
1    2008-08-25  Martin Maechler  <maechler@stat.math.ethz.ch>
2    
3            * src/dgCMatrix.c (dgCMatrix_LU): partially revert change
4            r2175 (2008-04-23) and do give an error for a singular matrix.
5            * R/Auxiliaries.R (detSparseLU): adapt to that.
6    
7            * R/LU.R: expand( <sparseLU> )
8    
9            * NAMESPACE, man/all.equal-methods.Rd:
10            * R/Matrix.R (all.equal): methods for Matrices,
11            * R/sparseMatrix.R, R/sparseVector.R: sparseMatrices and -Vectors
12    
13    
14    2008-08-23  Douglas Bates <bates@stat.wisc.edu>
15    
16            * [r2243] R/CHMfactor.R, man/CHMfactor-class.Rd: Added expand method and
17              documentation for CHMfactor class
18            * [r2241] R/CHMfactor.R: Added trivial coercion method for CHMfactor ->
19              pMatrix
20    
21    2008-08-19  Martin Maechler  <maechler@stat.math.ethz.ch>
22    
23            * R/nsCMatrix.R (setAs(., dgTMatrix))): remove unused method
24    
25    2008-08-18  Martin Maechler  <maechler@stat.math.ethz.ch>
26    
27            * R/Ops.R (.Ops2dge.via.x, and many others): eliminate never-used
28            variable assignments {from "next version" codetools}.
29            * R/Csparse.R, R/Tsparse.R: ditto
30    
31    2008-08-17  Martin Maechler  <maechler@stat.math.ethz.ch>
32    
33            * R/sparseVector.R (sp2vec, coerce to sparseVector):
34            make sure no integer overflows happen, and use double precision
35            (n, index) where appropriate.
36    
37            * tests/Simple.R: test "large" sparse vectors.
38    
39    2008-08-14  Martin Maechler  <maechler@stat.math.ethz.ch>
40    
41            * R/AllClass.R (sparseVector): 'length' and 'i' are "numeric", not
42            just integer (allowing much longer length).
43    
44    2008-07-28  Martin Maechler  <maechler@stat.math.ethz.ch>
45    
46            * R/AllClass.R (diagonalMatrix): extend  "sparseMatrix" instead of
47            "denseMatrix".  This renders "scarceMatrix" dispensable and
48            invalidates part of MM's presentations on "space of Matrix
49            classes", but seems cleaner overall.
50    
51            * R/diagMatrix.R, etc: eliminate "scarceMatrix", replacing it by
52            "sparseMatrix" in method signatures;
53            further, instead of coercing to "sparseMatrix", coerce to
54            "TsparseMatrix" now.
55    
56    2008-07-26  Martin Maechler  <maechler@stat.math.ethz.ch>
57    
58            * src/dgCMatrix.c (dgCMatrix_qrsol): allow third argument 'order' in
59            .Call(.)
60            * R/sparseMatrix.R (lm.fit.sparse), src/dgCMatrix.h, src/init.c: ditto
61    
62    2008-07-24  Martin Maechler  <maechler@stat.math.ethz.ch>
63    
64            * R/dgeMatrix.R: need solve(<dge>, <sparse>) against infinite
65            recursion in new test in
66            * tests/matprod.R: testing the above and another solve() case, below
67    
68            * R/sparseMatrix.R (lm.fit.sparse): slightly more efficient for
69            e.g. triangular 'x'.
70    
71            * src/dgCMatrix.c (dgCMatrix_qrsol): use AS_CSP() hence allowing dtC*
72            * src/dgCMatrix.c (dgCMatrix_cholsol): use AS_CHM_SP() to work
73            correctly with unit-triangular x
74    
75            * src/dsCMatrix.c (dsCMatrix_Csparse_solve): use AS_CHM_SP()
76            instead of not checking diagU.
77    
78            * R/diagMatrix.R, R/Auxiliaries.R: tweaks to allow later
79            experiments where diagonalMatrix would extend sparse*.
80    
81    
82    2008-07-23  Martin Maechler  <maechler@stat.math.ethz.ch>
83    
84            * src/dgCMatrix.c (compressed_non_0_ij): for nnzero(), use
85            "x@p[ncol(x)]" instead of length(x@i).
86            * R/Auxiliaries.R (nnzero): ditto
87    
88            * src/chm_common.c (as_cholmod_sparse): Do not use LENGTH(islot)
89            since that fails for over-allocated i.
90    
91            * tests/validObj.R: more testing of over-allocated (i,x) slots
92    
93    2008-07-23  Martin Maechler  <maechler@stat.math.ethz.ch>
94    
95            * src/chm_common.c (as_cholmod_sparse): Add 4th argument
96            'sort_in_place' and set it to TRUE in call from
97            * src/Csparse.c (Csparse_validate): sort in place, making sure that
98            validObject() continues sort the columns if needed.
99    
100            * tests/validObj.R: now tests that more thoroughly, and
101            * man/CsparseMatrix-class.Rd: documents it.
102    
103    2008-07-22  Douglas Bates <bates@stat.wisc.edu>
104    
105            * [r2233] src/chm_common.c: sort columns more carefully in
106              as_cholmod_sparse
107            * [r2231] src/chm_common.c: check for sorted columns in
108              as_cholmod_sparse instead of assuming it
109            * [r2228] src/cs_utils.c: Use R_alloc for semi-permanent storage when
110              expanding diagonal
111    
112    
113    2008-07-21  Martin Maechler  <maechler@stat.math.ethz.ch>
114    
115            * src/cs_utils.c (Matrix_as_cs): add check_Udiag switch
116            * src/cs_utils.h (AS_CSP & AS_CSP__): two versions
117            * src/dtCMatrix.c (dtCMatrix_sparse_solve): no longer needs
118            diagU2N().
119    
120            * R/diagMatrix.R (.sparseDiagonal): new utility, used in "old"
121            .spDiagonal() and new .trDiagonal().
122    
123            * R/dtCMatrix.R (solve): make use of .trDiagonal()
124    
125    2008-07-19  Martin Maechler  <maechler@stat.math.ethz.ch>
126    
127            * R/Auxiliaries.R (dimNamesCheck): fix very long standing buglet,
128            stumbled upon by Michael H.
129    
130            * tests/validObj.R: testing the bug-fix
131    
132            * src/chm_common.h (AS_CHM_SP__, AS_CHM_TR__): the non-diagU2N
133            versions.
134    
135            * src/chm_common.c (as_cholmod_sparse, as_cholmod_triplet): new
136            boolean argument 'check_Udiag' (formerly implicitly was FALSE).
137    
138            * src/Csparse.c (Csparse_Csparse_prod, ...): etc: use the new
139              AS_CHM_SP() which includes diagU2N.
140    
141            * inst/include/Matrix_stubs.c (M_as_cholmod_sparse): similarly
142            adapt to 3 arguments.
143    
144    2008-07-17  Douglas Bates <bates@stat.wisc.edu>
145    
146            * [r2220] src/dtCMatrix.c: Correct number of columns for rhs in
147              dtCMatrix_sparse_solve
148            * [r2219] src/cs_utils.c: eye->nz should be -1 for compressed column
149              storage
150            * [r2217] R/dtCMatrix.R, src/dtCMatrix.c, src/dtCMatrix.h, src/init.c:
151              Replace dtCMatrix_solve by more general dtCMatrix_sparse_solve and add
152              new solve method
153            * [r2216] src/cs_utils.c: Utility csp_eye in case we want to fold
154              Csparse_diagU2N functionality into Matrix_as_cs
155    
156    2008-07-17  Martin Maechler  <maechler@stat.math.ethz.ch>
157    
158            * inst/doc/factor2sparse.Rnw: revive a year-old unfinished vignette
159    
160    2008-07-16  Douglas Bates <bates@stat.wisc.edu>
161    
162            * [r2212] R/sparseMatrix.R: fac2sparse gets a drop.unused.levels
163              argument with default TRUE
164            * [r2211] inst/include/Matrix.h, inst/include/Matrix_stubs.c: Export
165              Csparse_diagU2N
166            * [r2210] R/dtCMatrix.R, man/dtCMatrix-class.Rd, src/dtCMatrix.c,
167              src/dtCMatrix.h, src/init.c: Remove vestigial methods based on the
168              parent array; new solve method for signature(a = "dtCMatrix", b =
169              "sparseMatrix")
170    
171    2008-07-14  Martin Maechler  <maechler@stat.math.ethz.ch>
172    
173            * R/diagMatrix.R (.bdiag): also keep result triangular
174    
175    2008-07-13  Douglas Bates <bates@stat.wisc.edu>
176    
177            * [r2208] src/dtCMatrix.c, src/dtTMatrix.c: Revise wording in error
178              messages
179    
180    2008-07-12  Martin Maechler  <maechler@stat.math.ethz.ch>
181    
182            * R/diagMatrix.R (.bdiag): make more sophisticated, keeping
183            symmetric- or nsparse-Matrix, also fixing the bug introduced with
184            the new version (.999375-10).
185    
186            * tests/Simple.R: regression test for the bugs.
187    
188    2008-07-07  Martin Maechler  <maechler@stat.math.ethz.ch>
189    
190            * R/sparseVector.R (spV2M): fix for "isparseVector".
191            Further, fix <diag> -> <sparseVector> coercion
192            (repSpV): add rep(<sparseVector>, .) method
193    
194            * R/sparseMatrix.R ([<-): when the RHS is a "scarce"Matrix, do *not*
195            use as.vector(.).
196    
197            * R/Tsparse.R ([<-): & [CR]sparse.R: methods for value = "sparseVector"
198    
199            * R/AllClass.R: new (hidden) class union "scarceMatrix"
200            * R/AllClass.R: sparseVector: add prototype
201    
202            * src/dsCMatrix.c (chk_nm): fix "Cholesky" check, thanks to
203            Kasper Kristensen
204    
205    2008-06-28  Martin Maechler  <maechler@stat.math.ethz.ch>
206    
207            * tests/other-pkgs.R: add more interesting Matrix -> graph
208    
209    2008-06-27  Martin Maechler  <maechler@stat.math.ethz.ch>
210    
211            * R/sparseMatrix.R (Tsp2grNEL): add 'need.uniq' argument for speed
212            improvement in "[CR]sparseMatrix" -> "graphNEL" coercion.
213    
214    2008-06-25  Martin Maechler  <maechler@stat.math.ethz.ch>
215    
216            * DESCRIPTION: release 0.999375-10 to CRAN
217    
218            * R/diagMatrix.R (.bdiag): use more efficient Bates-algorithm for
219            .bdiag().
220            * man/bdiag.Rd: update, including test.
221    
222    2008-06-24  Martin Maechler  <maechler@stat.math.ethz.ch>
223    
224            * tests/Simple.R: add minimal bdiag() checks
225    
226            * R/diagMatrix.R (bdiag): fix bdiag(diag(4:5)) case;
227              factor out the Tsparse - internal computation into new .bdiag()
228    
229    2008-06-14  Martin Maechler  <maechler@stat.math.ethz.ch>
230    
231            * R/nsparseMatrix.R: specific fast all() and any() methods.
232    
233            * src/dgTMatrix.c (MAKE_gTMatrix_to_geMatrix): better error message
234            when trying to produce too large result.
235    
236            * inst/test-tools.R (checkMatrix): add 'do.matrix' with a check for
237            very large matrices.
238    
239            * R/sparseMatrix.R (printSpMatrix2): new function, used by
240            show(<sparseMatrix>).
241    
242            * R/diagMatrix.R (show): print only diagonal entries when nrow(.) >= 50.
243    
244    2008-06-13  Martin Maechler  <maechler@stat.math.ethz.ch>
245    
246            * src/Mutils.c (m_encodeInd, m_encodeInd2):
247            * R/*.R: .Call(m_encodeInd2?, ..) instead of encodeInd2?(..).
248    
249            * R/Auxiliaries.R (encodeInd2?): care against integer overflow (for
250            big matrices): -> 2nd argument 'di' instead of 'nr' !
251    
252    2008-06-09  Martin Maechler  <maechler@stat.math.ethz.ch>
253    
254            * R/dtCMatrix.R: faster dgC* -> dtC* method
255            * tests/Simple.R: (hence removed "FIXME")
256    
257            * R/Auxiliaries.R (copyClass): add 'check = .copyClass.check'
258            which can be be turned off for possible speed gains.
259    
260    2008-06-02  Martin Maechler  <maechler@stat.math.ethz.ch>
261    
262            * R/dMatrix.R, R/Tsparse.R: get rid of some disambiguation warnings
263    
264            * R/not.R: fix !<ldiMatrix>
265            implement two old "FIXME"s:  !<ldenseMatrix> & !<ndenseMatrix>
266    
267            * R/diagMatrix.R (Ops): fix one-off thinko in
268            <diagonal> o <numeric> methods
269    
270            * inst/test-tools.R: checkMatrix(): drop0(m12) unconditionally
271    
272    2008-05-30  Martin Maechler  <maechler@stat.math.ethz.ch>
273    
274            * R/diagMatrix.R (Ops): more <diagonal> o <Matrix> methods
275            * tests/Simple.R: testing the above
276    
277    2008-05-07  Martin Maechler  <maechler@stat.math.ethz.ch>
278    
279            * NAMESPACE: also import "Ops" {found via new tools:::get_S4_generics_with_methods()}
280    
281    2008-05-03  Martin Maechler  <maechler@stat.math.ethz.ch>
282    
283            * R/Matrix.R (dimnames<-): dimnames(.) <- NULL works with a message;
284            * NAMESPACE (unname): finally exported
285    
286    2008-04-28  Martin Maechler  <maechler@stat.math.ethz.ch>
287    
288            * R/Auxiliaries.R (cholMat): possibly keep packed
289    
290            * inst/test-tools.R (checkMatrix): add fixed determinant.matrix()
291            for R < 2.7.0.
292    
293            * R/Tsparse.R ([): for triangularMatrix, check if result may be
294            triangular.
295            * tests/indexing.R: regression test
296    
297    2008-04-26  Martin Maechler  <maechler@stat.math.ethz.ch>
298    
299            * inst/test-tools.R (checkMatrix): test <Ops> not only for dMatrix
300            * R/Ops.R: more methods, for lMatrix/nMatrix
301    
302    2008-04-24  Martin Maechler  <maechler@stat.math.ethz.ch>
303    
304            * R/expm.R: new file for all expm() methods; notably new ones for
305            diagonal*, triangular*, symmetric* and also simple "matrix".
306    
307    2008-04-23  Martin Maechler  <maechler@stat.math.ethz.ch>
308    
309            * R/dsyMatrix.R: setAs(.) rather than setIs(.)  "to dpoMatrix"
310    
311            * inst/test-tools.R (assert.EQ.mat): better message when not equal
312    
313            * src/dgeMatrix.c (dgeMatrix_matrix_crossprod): allow integer RHS.
314    
315            * R/AllClass.R (ddiMatrix,ldiMatrix): extend [dl]Matrix instead of
316            [dl]denseMatrix {identical slots; but more logical method dispatch}
317    
318    2008-04-23  Martin Maechler  <maechler@stat.math.ethz.ch>
319    
320            * R/sparseMatrix.R (summary): use length(<i-slot>) instead of nnzero()
321    
322            * R/diagMatrix.R (determinant): method
323    
324    2008-04-22  Martin Maechler  <maechler@stat.math.ethz.ch>
325    
326            * src/dsCMatrix.c (dsCMatrix_Cholesky): suppress CHOLMOD printing too
327    
328            * R/Rsparse.R (.viaC.to.R): uplo fix for symmetric & triangular
329    
330            * R/dsCMatrix.R (determinant): switch to use Cholesky( 'LDL' ) and
331            its diagonal
332    
333    2008-04-21  Martin Maechler  <maechler@stat.math.ethz.ch>
334    
335            * R/dMatrix.R (Summary): short-cut for prod(<sparse>)
336    
337            * R/not.R: fix !<"U"-diag-ltrMatrix> ; drop {R < 2.6.0}-branch
338    
339            * R/Auxiliaries.R (tT2gT): fix for "U"-diag-ltTMatrix
340    
341            * R/AllClass.R: ltTMatrix validity: call (more stringent) tTMatrix_validate
342    
343    2008-04-19  Martin Maechler  <maechler@stat.math.ethz.ch>
344    
345            * R/Ops.R (Ops.x.x): aux.function, not just for (dMatrix,dMatrix)
346    
347            * R/Ops.R (.do.Logic.lsparse): fix NA case
348    
349            * R/Tsparse.R (replTmat): fix r.sym case, using indTri()
350    
351            * R/Auxiliaries.R (nnzero): fix special cases, using
352            * R/Auxiliaries.R (indDiag): new utility
353            * R/Auxiliaries.R (indTri): new argument 'diag'
354    
355            * R/dMatrix.R: Summmary(<ddenseMatrix>): different branch for dsy*
356    
357    2008-04-18  Martin Maechler  <maechler@stat.math.ethz.ch>
358    
359            * R/diagMatrix.R: "Summary" methods, and more "Arith" / "Ops"
360    
361            * src/Csparse.c (Csparse_drop): preserve (uplo,diag) for
362            ".tCMatrix" triangular matrix.
363    
364            * R/Auxiliaries.R (drop0): use diagU2N(); according to helpfile,
365            'clx' can be class *or* class representation.
366            (nnzSparse): new.
367            (non0ind): new 'xtendSymm' argument; used in
368            * R/Ops.R:
369    
370            * R/pMatrix.R: more efficient determinant() method
371    
372    2008-04-17  Martin Maechler  <maechler@stat.math.ethz.ch>
373    
374            * [disactivated] R/Matrix.R (det): det() as base::det(), but with Matrix environment
375            * [disactivated] NAMESPACE: export(det)
376    
377            * R/diagMatrix.R (mkDiag): new substitute for diag()
378    
379            * R/Auxiliaries.R (nnzero): fix for "diagU2N"-case
380            (as0, as1): new utility.
381    
382            * R/Csparse.R (diag, band): need diagU2N()
383    
384            * src/dgeMatrix.c (get_norm): return NA when 'x' slot has NA/NaN.
385    
386            * R/lMatrix.R: coerce(nMatrix |-> lMatrix) fix
387    
388            * R/Ops.R (Compare): fix <nsp> o <nsp> case
389    
390            * R/nsparseMatrix.R, R/pMatrix.R: is.na() method
391    
392    2008-04-16  Martin Maechler  <maechler@stat.math.ethz.ch>
393    
394            * R/Auxiliaries.R (signPerm): new utility for
395            * R/Auxiliaries.R (detSparseLU): determinant() via sparseLU
396    
397            * src/dsCMatrix.c (dsCMatrix_LDL_D): suppress 'CHOLMOD warning';
398            since we have our own error handler (and can use tryCatch() from R).
399    
400    2008-04-15  Martin Maechler  <maechler@stat.math.ethz.ch>
401    
402            * R/dgTMatrix.R (image): ha! set col=NA if lwd is small -- very nice!
403    
404            * R/dsCMatrix.R (determinant): use tryCatch() and switch to lu()
405            when not positive definite.
406    
407            * R/Auxiliaries.R (asTri): new auxiliary
408            (non0.i): make *much* faster for Tsparse with many non-zero
409            entries; add 'uniqT = TRUE' argument to be used when sorting is undesired.
410    
411            * tests/Class+Meth.R (dotestMat): now build on checkMatrix() from
412            test-tools.R , see below
413    
414            * R/dMatrix.R: fix "Summary" method: + diagU2N()
415    
416            * NAMESPACE, R/Matrix.R: add mean() method
417    
418    2008-04-12  Martin Maechler  <maechler@stat.math.ethz.ch>
419    
420            * R/dgTMatrix.R (image): allow to *not* take abs(), and use
421            cold-hot colors; try *changed* default useAbs = FALSE
422            * man/image-methods.Rd:  nice examples
423    
424    2008-04-11  Martin Maechler  <maechler@stat.math.ethz.ch>
425    
426            * inst/test-tools.R (checkMatrix): new function for modularizing part
427            of tstMatrixClass() in tests/Class+Meth.R
428    
429            * R/dsCMatrix.R: coercion from "matrix"
430            * R/ltTMatrix.R, R/ntTMatrix.R: ditto (change it).
431    
432            * tests/Class+Meth.R (tstMatrixClass): some cleanup;
433            add test for as(matrix(,0,0), <class>)
434    
435    2008-04-09  Martin Maechler  <maechler@stat.math.ethz.ch>
436    
437            * src/dgeMatrix.c (dgeMatrix_determinant): for n == 0,
438            work as determinant(matrix(,0,0)).
439    
440            * src/dgCMatrix.c (dgCMatrix_LU): return {L,U} as dtCMatrix
441            * man/sparseLU-class.Rd: ditto
442    
443            * R/dgCMatrix.R (determinant): method building on lu()
444            * R/sparseMatrix.R, Matrix.R, ...: ditto
445    
446            * R/Auxiliaries.R (mkDet): auxiliary for determinant()
447    
448    2008-04-07  Martin Maechler  <maechler@stat.math.ethz.ch>
449    
450            * R/sparseMatrix.R (summary<sparseMatrix>): no 'x' column for
451            pattern matrices.
452    
453    2008-04-02  Martin Maechler  <maechler@stat.math.ethz.ch>
454    
455            * src/dense.c (dense_to_Csparse): all declarations *before*
456            R_CheckStack(); needed e.g. for ancient gcc 2.96.
457    
458    
459  2008-03-29  Martin Maechler  <maechler@stat.math.ethz.ch>  2008-03-29  Martin Maechler  <maechler@stat.math.ethz.ch>
460    
461          * DESCRIPTION (Version): 0.999375-9 --- need to release          * DESCRIPTION (Version): 0.999375-9 --- need to release
462          for R-devel (and R 2.7.0 alpha soon).          for R-devel (and R 2.7.0 alpha soon).
463    
464            * R/AllClass.R: drop "double" from "atomicVector" class union
465    
466            * R/AllGeneric.R (rcond): check for base::rcond instead of R version
467            * R/dgeMatrix.R: ditto
468    
469          * R/sparseMatrix.R (summary): count NAs          * R/sparseMatrix.R (summary): count NAs
470    
471            * inst/doc/Intro2Matrix.Rnw: changes, aim for *one* introduction.
472    
473  2008-03-28  Martin Maechler  <maechler@stat.math.ethz.ch>  2008-03-28  Martin Maechler  <maechler@stat.math.ethz.ch>
474    
475          * R/AllGeneric.R: rcond(., norm) instead of rcond(., type), in          * R/AllGeneric.R: rcond(., norm) instead of rcond(., type), in

Legend:
Removed from v.2159  
changed lines
  Added in v.2247

root@r-forge.r-project.org
ViewVC Help
Powered by ViewVC 1.0.0  
Thanks to:
Vienna University of Economics and Business Powered By FusionForge