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Diff of /pkg/TODO

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revision 530, Mon Feb 7 10:58:27 2005 UTC revision 935, Tue Sep 20 10:14:57 2005 UTC
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1    - Sparse matrix methods can now be based on the CHOLMOD package.  We
2       will need to migrate from the current code to CHOLMOD-based code
3       using #ifdef USE_CHOLMOD.  Some of the things to be done
4    
5       - Move documentation from subdirectories of src to inst/doc
6       - Write utilities to create a cholmod_sparse pointer from a
7       dgCMatrix or lgCMatrix (or zgCMatrix) object without copying and
8       allocating.
9       - Start adding simple S4 methods (rcond, %*%, +, cbind, t).
10    
11  - Report the problem in the Linux ldexp manual page.  The second and  - Report the problem in the Linux ldexp manual page.  The second and
12    third calls in the Synopsis should be to ldexpf and ldexpl.    third calls in the Synopsis should be to ldexpf and ldexpl.
13    
14  - [,] indexing  - [,] indexing: for sparse "works", but not yet for negative indices!
15    
16  - group generics: "Arith", but also "Ops" and "Math";  see  - group generics: "Arith" (partly done),
17    ?Math.data.frame  and the examples in    but also "Compare", "Math" etc;
18    ?SetGeneric    see ?Math  and the examples in ?SetGeneric
19    
20  - bCrosstab(): do we really want the diagonal "V:V" crosstabs?  - methods for rbind and cbind where they make sense
21                 (if so or in any case: add to  man/bCrosstab.Rd )    (Kurt is particularly interested in dgCMatrix ones, for pkg 'arules')
22      ****> UNFEASIBLE as long cbind is function(..., *) !!!! <*******
23        --> follow John's proposition  cbind(x, ...) via Generic cbind2(x,y)?
24    
25  - src/Metis/ : one of the two Makefiles needs fixing, as changing  - consider moving alloc3Darray from ./src/Mutils.c to
26               src/Metis/*.c  does not lead to recompilation.    $(RSRC)/src/base/array.c
   --DB - it seems both Makefiles need fixing.  I think I have the  
              src/Metis/Makefile fixed but not src/Makefile  
27    
28  - man/Matrix.Rd :  has example with dimnames, but we just drop them!  -  slot "factors" maybe should move up to "Matrix"
                 MM thinks dimnames should be supported (but then ...)  
29    
30  - data/ : names 'mm' and even more 'y' are  ``too short''.  -------
         If we really want to keep them, don't use "LazyData"  
         (such that one needs  data(*) explicitly);  
         But MM would rather want something like  ex.mm and ex.y  
31    
32  - "factors" maybe should move up to "Matrix"  - provide methods for "dspMatrix" and "dppMatrix"!
33    
34  -------  - implement (more) methods for supporting "packed" (symmetric / triangular)
35      matrices; particularly something like pack() and unpack()  [to/from our
36      classes from/to "numeric"] --- have already man/unpack.Rd but no method yet!
37    
38      (have some dtr* <-> dtp*)
39    
40    - implement diagonal Matrix class  "ddiMatrix" etc
41      using constructor function Diagonal() or Diag().
42    
43    BUG: rcond() of a singular dpoMatrix gives a LaPack error instead of just 0:
44      MM <- crossprod(M <- Matrix(c(1:4,9:6), 2,4)) ; rcond(MM)
45      ##> Error in rcond(MM) : Lapack routine dpotrf returned error code 4
46    
47    
48    ---
49    
50    - combine the C functions for multiplication by special forms and
51      solution wrt special forms by using a 'right' argument and a
52      'classed' argument.
53       [done with dgeMatrix_matrix_mm();  not yet for other classes;
54        and for _crossprod()]
55    
56    - add more comprehensive examples / tests for Schur decomposition
57    
58    - arithmetic for sparse matrices:
59                 <sparseMatrix>  o  <same-dim-sparseMatrix>
60      should return a sparse matrix  for at least "+" and "*" , also %%,
61      and "/" and "%/%" at least when the RHS is non-zero a scalar.
62      Challenge: nice implementation (``common non-0''; but Tsparse* is not uniq).
63    
64    ---
65    
66  We have a (at least one) basic problem :  - Create a Harwell-Boeing version of the matrix mm and the response
67     Currently the show() method fail sometime after coercion:    vector y in inst/external and remove them from the data directory.
68     e.g. 'sy' show()s wrongly, even though it "str()" fine :    Modify any examples that use them and modify the Comparisons vignette.
   
       (po <- crossprod(Matrix(0:3, 2))) # ok  
       (ge <- as(po, "dgeMatrix")) # ok  
       (sy <- as(po, "dsyMatrix")) # BAD  
       str(sy) # looks fine  
   
   or  
       example(expand) # -> ex$L and ex$U look bad, however  
       as(ex$L, "dgeMatrix") # `works'  
69    
70    {Of course, we don't need a workaround but must understand  - "Math2" , "Math", "Arith":
71     and solve the problem}     keep triangular and symmetric Matrices when appropriate:
72       particularly desirable for  "Math2": round(), signif()

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