 pkg/TODO 2005/03/15 00:51:42 645
+++ pkg/TODO 2007/06/07 09:04:34 1887
@@ 1,59 +1,153 @@
+Check for DimNames propagation in coercion and other operations.
+
+ rcond methods for sparseMatrix classes
+
 Report the problem in the Linux ldexp manual page. The second and
third calls in the Synopsis should be to ldexpf and ldexpl.
 [,] indexing

 group generics: "Arith" (partly done),
 but also "Compare", "Math" etc;
 see ?Math and the examples in ?SetGeneric

 methods for rbind and cbind where they make sense
+ [,] indexing: for sparse "works", but not yet for negative indices!
 consider moving alloc3Darray from ./src/Mutils.c to
$(RSRC)/src/base/array.c

 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

 slot "factors" maybe should move up to "Matrix"



We have a (at least one) basic problem :
 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'

 {Of course, we don't need a workaround but must understand
 and solve the problem}



+
 provide methods for "dspMatrix" and "dppMatrix"!
 implement (more) methods for supporting "packed" (symmetric / triangular)
matrices; particularly something like pack() and unpack() [to/from our
classes from/to "numeric"]  have already man/unpack.Rd but no method yet!
 implement diagonal Matrix class "ddiMatrix" etc
 using constructor function Diagonal() or Diag().
+ (have some dtr* <> dtp*)


 create a class of permutation matrices for use in expand. The
 current expand method for the LU factorization is not complete
 because it does not provide the permutation.
+
 combine the C functions for multiplication by special forms and
solution wrt special forms by using a 'right' argument and a
'classed' argument.
+ [done with dgeMatrix_matrix_mm(); not yet for other classes;
+ and for _crossprod()]
+
+ add more comprehensive examples / tests for Schur decomposition
+
+ arithmetic for sparse matrices:
+ o
+ should return a sparse matrix for at least "+" and "*" , also %%,
+ and "/" and "%/%" at least when the RHS is nonzero a scalar.
+ Challenge: nice implementation (``common non0''; but Tsparse* is not uniq).
+
+
+
+ "Math2" , "Math", "Arith":
+ keep triangular and symmetric Matrices when appropriate:
+ particularly desirable for "Math2": round(), signif()
+
+ "d" <> "l" coercion for all "[TCR]" sparse matrices is really trivial:
+ "d" > "l" : drops the 'x' slot
+ "l" > "d" : construct an 'x' slot of all '1'
+ We currently have many of these conversions explicitly, e.g.
+ setAs("dsTMatrix", "lsTMatrix",
+ function(from) new("lsTMatrix", i = from@i, j = from@j, uplo = from@uplo,
+ Dim = from@Dim, Dimnames = from@Dimnames))
+ but I would rather want to automatically construct all these coercion
+ methods at once by a ``method constructor'', i.e.,
+ for all "dsparse*" > "lsparse*" and vice versa.
+ How can one do this {in a documented way} ?
+
+ tcrossprod(x, y) : do provide methods for y != NULL
+ calling Lapack's DGEMM for "dense"
+ [200512xx: done for dgeMatrix at least]
+
+ BUGlet: Shouldn't lose factorization here:
+ h6 < Hilbert(6); chol(h6) ; str(h6) # has factor
+ str(H6 < as(h6, "dspMatrix")) # has lost factor
+ ## and the same in a similar situation involving "dpo", "dpp"
+
+ Things like M[upper.tri(M)] are not really most useful for sparse
+ matrices. > provide generic functions
+ upperTriMatrix(), lowerTriMatrix() both with argument 'diag = TRUE'
+ (which can be set to FALSE of course) which are used to extract a
+ triangle from an arbitrary sparse matrix and return a "dtCMatrix".
+
+ Factorizations: LU done; also Schur() for *sparse* Matrices.
+
+ band(), triu(), tril() for *all* including "matrix", not just sparse matrices
+
+ is.na() method for all our matrices [ ==> which(*, arr.ind=TRUE) might work ]
+
+ When we have a packed matrix, it's a waste to go through "full" to "sparse":
+ ==> implement
+ setAs("dspMatrix", "sparseMatrix")
+ setAs("dppMatrix", "sparseMatrix")
+ setAs("dtpMatrix", "sparseMatrix")
+ and the same for "lsp" , "ltp" and "nsp" , "ntp" !
+
+ use .Call(Csparse_drop, M, tol) in more places,
+ both with 'tol = 0.' to drop "values that happen to be 0" and for
+ zapsmall() methods for Csparse*
+
+ implement .Call(Csparse_scale, ....) interfacing to cholmod_scale()
+ in src/CHOLMOD/Include/cholmod_matrixops.h : for another function
+ specifically for multiplying a cholmod_sparse object by a diagonal matrix.
+ Use it in %*% and [t]crossprod methods.
+
+ chol() and determinant() should ``work'': proper result or "good" error
+ message.
+
+ Think of constructing setAs(...) calls automatically in order to
+ basically enable all ``sensible'' as(fromMatrix, toMatrix) calls,
+ possibly using canCoerce(.)
+
+ make sure *all* group methods have (maybe "bailout") setMethod for "Matrix".
+ e.g. zapsmall() fails "badly"
+
+ speedup: pass class definition to non0ind() [check all calls ..]
+
+ sum(): implement methods which work for *all* our matrices.
+
+ Implement expand(.) for the Cholesky() results
+ "dCHMsimpl" and "dCHMsuper"  currently have no *decent* way to get at
+ the matrix factors of the corresponding matrix factorization !!
+
+ rbind(, ) does not work (e.g. , )
+
+ setAs(, "[dln]Matrix" ) for in {Matrix or denseMatrix + sparseMatrix}
+
+ Tell users about the possibility to disable the "S4generic but somewhat slow"
+ cbind/rbind, e.g. via
+
+ setHook(packageEvent("Matrix", "onLoad"),
+ function(...) methods:::bind_activation(FALSE))
+
+ ensure that M[0], M[FALSE], M[1:2] works as for traditional Matrices
+
+ make sure M[FALSE, FALSE] works for all Matrices
+ {e.g. fails for M < Diagonal(4)}
+
+ %*% {also in crossprod/tcrossprod} currently always
+ returns , since > Csparse_dense_prod > cholmod_sdmult
+ and that does only return dense.
+ When the sparse matrix is very sparse, i.e. has many rows with only zero
+ entries, it would make much sense to return sparse.
+
+ sparsesymmetric + diagonal should stay sparsesymmetric
+ (only stays sparse): Matrix(0, 4, 4) + Diagonal(4, 1:4)
+ > R/diagMatrix.R ('FIXME')
+ but also R/Ops.R to ensure spsym. + spsym. > spsym. etc
+
+ For a square sparse matrix 'b' {typically dgCMatrix or dgTMatrix},
+ we'd want a function "Mat_plus_t_Mat" < function(b) {....}
+ which computes the symmetric sparse matrix b + t(b)
+ in way that never works with sizedoubled vectors from b@i etc..
+
+ ! loses symmetry, both for dense and sparse matrices.
+ !M where M is "sparseMatrix", currently always gives dense. This only
+ makes sense when M is ``really sparse''.
+
+ column names of sparse matrices are not printed;
+ we now "mention" them (if they are nonempty).
+ Option:
+ build show( ) on a function, possibly
+ print.sparseMatrix(), which gets an argument such as
+ 'col.names.show = FALSE' which is documented and can be set to TRUE
+
+ 'arules' needs fast colSums() and rowSums()  for ngCMatrix;
+ do it for "nMatrix" and "lMatrix" and return *integer*