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Diff of /pkg/TODO

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revision 529, Mon Feb 7 10:56:34 2005 UTC revision 953, Wed Sep 28 19:31:36 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    - methods for rbind and cbind where they make sense
21      (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  - bCrosstab(): do we really want the diagonal "V:V" crosstabs?  - consider moving alloc3Darray from ./src/Mutils.c to
26                 (if so or in any case: add to  man/bCrosstab.Rd )    $(RSRC)/src/base/array.c
27    
28  - src/Metis/ : one of the two Makefiles needs fixing, as changing  -------
              src/Metis/*.c  does not lead to recompilation.  
   --DB - it seems both Makefiles need fixing.  I think I have the  
              src/Metis/Makefile fixed but not src/Makefile  
29    
30  - man/Matrix.Rd :  has example with dimnames, but we just drop them!  - provide methods for "dspMatrix" and "dppMatrix"!
                 MM thinks dimnames should be supported (but then ...)  
31    
32  - data/ : names 'mm' and even more 'y' are  ``too short''.  - implement (more) methods for supporting "packed" (symmetric / triangular)
33          If we really want to keep them, don't use "LazyData"    matrices; particularly something like pack() and unpack()  [to/from our
34          (such that one needs  data(*) explicitly);    classes from/to "numeric"] --- have already man/unpack.Rd but no method yet!
         But MM would rather want something like  ex.mm and ex.y  
35    
36  - spelling style: Should "coersion" be "coercion" ?    (have some dtr* <-> dtp*)
37    
38  - "factors" maybe should move up to "Matrix"  - implement diagonal Matrix class  "ddiMatrix" etc
39      using constructor function Diagonal() or Diag().
40    
41  -------  BUG: rcond() of a singular dpoMatrix gives a LaPack error instead of just 0:
42      MM <- crossprod(M <- Matrix(c(1:4,9:6), 2,4)) ; rcond(MM)
43      ##> Error in rcond(MM) : Lapack routine dpotrf returned error code 4
44    
45    
46    ---
47    
48    - combine the C functions for multiplication by special forms and
49      solution wrt special forms by using a 'right' argument and a
50      'classed' argument.
51       [done with dgeMatrix_matrix_mm();  not yet for other classes;
52        and for _crossprod()]
53    
54    - add more comprehensive examples / tests for Schur decomposition
55    
56    - arithmetic for sparse matrices:
57                 <sparseMatrix>  o  <same-dim-sparseMatrix>
58      should return a sparse matrix  for at least "+" and "*" , also %%,
59      and "/" and "%/%" at least when the RHS is non-zero a scalar.
60      Challenge: nice implementation (``common non-0''; but Tsparse* is not uniq).
61    
62    ---
63    
64  We have a (at least one) basic problem :  - Create a Harwell-Boeing version of the matrix mm and the response
65     Currently the show() method fail sometime after coercion:    vector y in inst/external and remove them from the data directory.
66     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'  
67    
68    {Of course, we don't need a workaround but must understand  - "Math2" , "Math", "Arith":
69     and solve the problem}     keep triangular and symmetric Matrices when appropriate:
70       particularly desirable for  "Math2": round(), signif()

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