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revision 530, Mon Feb 7 10:58:27 2005 UTC revision 1290, Thu Jun 8 09:30:21 2006 UTC
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1    -----
2    Modify the one-argument form of the anova method for lmer objects (yet
3      again) to calculate the F ratios.  It is the df, not the ratio that
4      is controversial.
5    Should there be an extractor function for the mean square error?  If
6    so,
7    -----
8    Check for DimNames propagation in coercion and other operations.
9    -----
10    - Revive the "lmer" and "glmer" classes.  Slots like "family" should
11      be in "glmer" only.  Many methods for "lmer" can be simplified as,
12      for example, they will always use the scale factor.
13    
14    - Add a "pedigree" class and methods for it.  Allow a pedigree
15      argument in lmer.
16    
17    ------
18    - Sparse matrix methods can now be based on the CHOLMOD package.  We
19       will need to migrate from the current code to CHOLMOD-based code
20       using #ifdef USE_CHOLMOD.  Some of the things to be done
21    
22       - Move documentation from subdirectories of src to inst/doc
23       - Write utilities to create a cholmod_sparse pointer from a
24       dgCMatrix or lgCMatrix (or zgCMatrix) object without copying and
25       allocating.
26       - Start adding simple S4 methods (rcond, %*%, +, cbind, t).
27    
28  - Report the problem in the Linux ldexp manual page.  The second and  - Report the problem in the Linux ldexp manual page.  The second and
29    third calls in the Synopsis should be to ldexpf and ldexpl.    third calls in the Synopsis should be to ldexpf and ldexpl.
30    
31  - [,] 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 )  
32    
33  - src/Metis/ : one of the two Makefiles needs fixing, as changing  - consider moving alloc3Darray from ./src/Mutils.c to
34               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  
35    
36  - 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  
37    
38  - "factors" maybe should move up to "Matrix"  - provide methods for "dspMatrix" and "dppMatrix"!
39    
40  -------  - implement (more) methods for supporting "packed" (symmetric / triangular)
41      matrices; particularly something like pack() and unpack()  [to/from our
42      classes from/to "numeric"] --- have already man/unpack.Rd but no method yet!
43    
44      (have some dtr* <-> dtp*)
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    - "Math2" , "Math", "Arith":
65       keep triangular and symmetric Matrices when appropriate:
66       particularly desirable for  "Math2": round(), signif()
67    
68    - "d" <-> "l" coercion for all "[TCR]" sparse matrices is really trivial:
69      "d" -> "l" : drops the 'x' slot
70      "l" -> "d" : construct an 'x' slot of all '1'
71      We currently have many of these conversions explicitly, e.g.
72       setAs("dsTMatrix", "lsTMatrix",
73          function(from) new("lsTMatrix", i = from@i, j = from@j, uplo = from@uplo,
74                             Dim = from@Dim, Dimnames = from@Dimnames))
75      but I would rather want to automatically construct all these coercion
76      methods at once by a ``method constructor'', i.e.,
77      for all  "dsparse*" -> "lsparse*" and vice versa.
78      How can one do this {in a documented way} ?
79    
80    - tcrossprod(x, y) : do provide methods for y != NULL
81      calling Lapack's DGEMM for "dense"
82      [2005-12-xx: done for dgeMatrix at least]
83    
84    - "ltTmatrix" :
85      2) new("ltTMatrix", diag = "U", Dim = c(2:2, 2:2)) shows lack of ltTM*_validate
86    
87    - BUGlet:  Shouldn't lose factorization here:
88      h6 <- Hilbert(6); chol(h6) ; str(h6) # has factor
89      str(H6 <- as(h6, "dspMatrix"))       # has lost factor
90      ## and the same in a similar situation involving  "dpo", "dpp"
91    
92    - "Compare" for dgC & dgT  --- want to be able to do  M[M > 10]  etc
93    
94    - Things like  M[upper.tri(M)] are not really most useful for  sparse
95      matrices.  --> provide generic functions
96      upperTriMatrix(), lowerTriMatrix()  both with argument  'diag = TRUE'
97      (which can be set to FALSE of course) which are used to extract a
98      triangle from an arbitrary sparse matrix and  return a  "dtCMatrix".
99    
100    - Factorizations: LU [ -> solve() ] and Schur()  for  *sparse*  Matrices.
101      -----------------  LU-sparse is the purpose of all of ./src/UMFPACK/
102            -->  ./inst/doc/UFsparse/*
103      And then, possibly eigen(), svd(), qr(), ... for sparse
104      {probably base some on the fast  chol() of CHOLMOD}.
105    
106  We have a (at least one) basic problem :    2006-04-15 : now with 'CSparse' { src/cs.c }, have at least solve( <dtC*> )
    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'  
107    
108    {Of course, we don't need a workaround but must understand  - nicer pedigree examples and tests
    and solve the problem}  

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