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[matrix] Diff of /pkg/TODO
 [matrix] / pkg / TODO

Diff of /pkg/TODO

revision 491, Wed Feb 2 19:40:26 2005 UTC revision 1887, Thu Jun 7 09:04:34 2007 UTC
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1    Check for DimNames propagation in coercion and other operations.
2    ------
3    - rcond methods for sparseMatrix classes
4
5  - Report the problem in the Linux ldexp manual page.  The second and  - Report the problem in the Linux ldexp manual page.  The second and
6    third calls in the Synopsis should be to ldexpf and ldexpl.    third calls in the Synopsis should be to ldexpf and ldexpl.
7
8  - [,] indexing  - [,] indexing: for sparse "works", but not yet for negative indices!
9
10    - consider moving alloc3Darray from ./src/Mutils.c to
11      \$(RSRC)/src/base/array.c
12    ------
13    - provide methods for "dspMatrix" and "dppMatrix"!
14
15    - implement (more) methods for supporting "packed" (symmetric / triangular)
16      matrices; particularly something like pack() and unpack()  [to/from our
17      classes from/to "numeric"] --- have already man/unpack.Rd but no method yet!
18
19      (have some dtr* <-> dtp*)
20
21    -----
22
23    - combine the C functions for multiplication by special forms and
24      solution wrt special forms by using a 'right' argument and a
25      'classed' argument.
26       [done with dgeMatrix_matrix_mm();  not yet for other classes;
27        and for _crossprod()]
28
29    - add more comprehensive examples / tests for Schur decomposition
30
31    - arithmetic for sparse matrices:
32                 <sparseMatrix>  o  <same-dim-sparseMatrix>
33      should return a sparse matrix  for at least "+" and "*" , also %%,
34      and "/" and "%/%" at least when the RHS is non-zero a scalar.
35      Challenge: nice implementation (``common non-0''; but Tsparse* is not uniq).
36
37    -----
38
39    - "Math2" , "Math", "Arith":
40       keep triangular and symmetric Matrices when appropriate:
41       particularly desirable for  "Math2": round(), signif()
42
43    - "d" <-> "l" coercion for all "[TCR]" sparse matrices is really trivial:
44      "d" -> "l" : drops the 'x' slot
45      "l" -> "d" : construct an 'x' slot of all '1'
46      We currently have many of these conversions explicitly, e.g.
47       setAs("dsTMatrix", "lsTMatrix",
48          function(from) new("lsTMatrix", i = from@i, j = from@j, uplo = from@uplo,
49                             Dim = from@Dim, Dimnames = from@Dimnames))
50      but I would rather want to automatically construct all these coercion
51      methods at once by a ``method constructor'', i.e.,
52      for all  "dsparse*" -> "lsparse*" and vice versa.
53      How can one do this {in a documented way} ?
54
55    - tcrossprod(x, y) : do provide methods for y != NULL
56      calling Lapack's DGEMM for "dense"
57      [2005-12-xx: done for dgeMatrix at least]
58
59    - BUGlet:  Shouldn't lose factorization here:
60      h6 <- Hilbert(6); chol(h6) ; str(h6) # has factor
61      str(H6 <- as(h6, "dspMatrix"))       # has lost factor
62      ## and the same in a similar situation involving  "dpo", "dpp"
63
64    - Things like  M[upper.tri(M)] are not really most useful for  sparse
65      matrices.  --> provide generic functions
66      upperTriMatrix(), lowerTriMatrix()  both with argument  'diag = TRUE'
67      (which can be set to FALSE of course) which are used to extract a
68      triangle from an arbitrary sparse matrix and  return a  "dtCMatrix".
69
70    - Factorizations: LU done; also Schur()  for  *sparse*  Matrices.
71
72    - band(), triu(), tril() for *all* including "matrix", not just sparse matrices
73
74    - is.na() method for all our matrices [ ==> which(*, arr.ind=TRUE) might work ]
75
76    - When we have a packed matrix, it's a waste to go through "full" to "sparse":
77      ==> implement
78            setAs("dspMatrix", "sparseMatrix")
79            setAs("dppMatrix", "sparseMatrix")
80            setAs("dtpMatrix", "sparseMatrix")
81      and the same for "lsp" , "ltp"  and  "nsp" , "ntp" !
82
83    - use  .Call(Csparse_drop, M, tol) in more places,
84      both with 'tol = 0.' to drop "values that happen to be 0" and for
85      zapsmall() methods for Csparse*
86
87    - implement .Call(Csparse_scale, ....) interfacing to cholmod_scale()
88      in src/CHOLMOD/Include/cholmod_matrixops.h : for another function
89      specifically for multiplying a cholmod_sparse object by a diagonal matrix.
90      Use it in %*% and [t]crossprod methods.
91
92    - chol() and determinant() should ``work'': proper result or "good" error
93      message.
94
95    - Think of constructing  setAs(...) calls automatically in order to
96      basically enable all ``sensible'' as(fromMatrix, toMatrix)  calls,
97      possibly using canCoerce(.)
98
99    - make sure *all* group methods have (maybe "bail-out") setMethod for "Matrix".
101
102    - speedup: pass class definition to non0ind() [check all calls ..]
103
104    - sum(): implement methods which work for *all* our matrices.
105
106    - Implement  expand(.) for the Cholesky() results
107      "dCHMsimpl" and  "dCHMsuper"  -- currently have no *decent* way to get at
108      the matrix factors of the corresponding matrix factorization !!
109
110    - rbind(<sparse>, <dense>) does not work  (e.g. <dgC>, <dge>)
111
112    - setAs(<Mcl>,  "[dln]Matrix" )  for <Mcl> in {Matrix or denseMatrix + sparseMatrix}
113
114    - Tell users about the possibility to disable the "S4-generic but somewhat slow"
115      cbind/rbind, e.g. via
116
118              function(...) methods:::bind_activation(FALSE))
119
120    - ensure that  M[0], M[FALSE], M[1:2]  works as for traditional Matrices
121
122  - group generics: "Arith", but also "Ops" and "Math";  see  - make sure  M[FALSE, FALSE]  works for all Matrices
123    ?Math.data.frame  and the examples in    {e.g. fails for M <- Diagonal(4)}
?SetGeneric
124
125  - check to see if the .onLoad function to require the methods package  - <sparse> %*% <dense>  {also in crossprod/tcrossprod}  currently always
126    (in the AllClass.R file) is needed    returns <dense>, since --> Csparse_dense_prod --> cholmod_sdmult
127      and that does only return dense.
128      When the sparse matrix is very sparse, i.e. has many rows with only zero
129      entries, it would make much sense to return sparse.
130
131  - Should the uplo and diag slots continue to be stored as character?  - sparse-symmetric + diagonal should stay sparse-symmetric
132    An alternative is to use a factor as in the enum values for the    (only stays sparse): Matrix(0, 4, 4) + Diagonal(4, 1:4)
133    cblas.    --> R/diagMatrix.R ('FIXME')
134      but also R/Ops.R  to ensure  sp-sym. + sp-sym. |-> sp-sym.  etc
135
136  - Organization of the source code files - right now they are organized  - For a square sparse matrix 'b' {typically dgCMatrix or dgTMatrix},
137    according to class (e.g. dgeMatrix.R, dgeMatrix.h, dgeMatrix.c).  Is    we'd want a function  "Mat_plus_t_Mat" <- function(b) {....}
138    there a better way?    which computes the symmetric sparse matrix   b + t(b)
139      in way that never works with size-doubled vectors from  b@i etc..
140
141  - Fix the calculation of the Dim slot for the crossprod method for  - ! <symmetricMatrix>  loses symmetry, both for dense and sparse matrices.
142    dgCMatrix objects (too tired to do that now).    !M  where M is "sparseMatrix", currently always gives dense. This only
143      makes sense when M is ``really sparse''.
144
145    - column names of sparse matrices are not printed;
146      we now "mention" them (if they are non-empty).
147      Option:
148            build show( <sparseMatrix>) on a function, possibly
149            print.sparseMatrix(), which gets an argument such as
150            'col.names.show  = FALSE' which is documented and can be set to TRUE
151
152    - 'arules' needs fast colSums() and rowSums() - for ngCMatrix;
153      do it for "nMatrix" and "lMatrix" and return *integer*

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