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revision 529, Mon Feb 7 10:56:34 2005 UTC revision 956, Fri Sep 30 17:28:00 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!
   
 - group generics: "Arith", but also "Ops" and "Math";  see  
   ?Math.data.frame  and the examples in  
   ?SetGeneric  
   
 - bCrosstab(): do we really want the diagonal "V:V" crosstabs?  
                (if so or in any case: add to  man/bCrosstab.Rd )  
   
 - 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  
   
 - man/Matrix.Rd :  has example with dimnames, but we just drop them!  
                 MM thinks dimnames should be supported (but then ...)  
   
 - 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  
15    
16  - spelling style: Should "coersion" be "coercion" ?  - group generics: "Arith" (partly done),
17      but also "Compare", "Math" etc;
18      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  - "factors" maybe should move up to "Matrix"  - consider moving alloc3Darray from ./src/Mutils.c to
26      $(RSRC)/src/base/array.c
27    
28  -------  -------
29    
30  We have a (at least one) basic problem :  - provide methods for "dspMatrix" and "dppMatrix"!
    Currently the show() method fail sometime after coercion:  
    e.g. 'sy' show()s wrongly, even though it "str()" fine :  
   
       (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'  
31    
32    {Of course, we don't need a workaround but must understand  - implement (more) methods for supporting "packed" (symmetric / triangular)
33     and solve the problem}    matrices; particularly something like pack() and unpack()  [to/from our
34      classes from/to "numeric"] --- have already man/unpack.Rd but no method yet!
35    
36      (have some dtr* <-> dtp*)
37    
38    - 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    - Create a Harwell-Boeing version of the matrix mm and the response
65      vector y in inst/external and remove them from the data directory.
66      Modify any examples that use them and modify the Comparisons vignette.
67    
68    - "Math2" , "Math", "Arith":
69       keep triangular and symmetric Matrices when appropriate:
70       particularly desirable for  "Math2": round(), signif()
71    
72    - "d" <-> "l" coercion for all "[TCR]" sparse matrices is really trivial:
73      "d" -> "l" : drops the 'x' slot
74      "l" -> "d" : construct an 'x' slot of all '1'
75      We currently have many of these conversions explicitly, e.g.
76       setAs("dsTMatrix", "lsTMatrix",
77          function(from) new("lsTMatrix", i = from@i, j = from@j, uplo = from@uplo,
78                             Dim = from@Dim, Dimnames = from@Dimnames))
79      but I would rather want to automatically construct all these coercion
80      methods at once by a ``method constructor'', i.e.,
81      for all  "dsparse*" -> "lsparse*" and vice versa.
82      How can one do this {in a documented way} ?

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