The R Project SVN R-packages

- check to see if the .onLoad function to require the methods package
  (in the AllClass.R file) is needed
  -- no, it is not:  "Depends: " in DESCRIPTION suffices.

- Should the uplo and diag slots continue to be stored as character?
  An alternative is to use a factor as in the enum values for the
  cblas.
  -- Leave as character but use care in determining the default cases
  -- E.g. Checks for diag slot should check for 'U' or 'u' vs. anything else

- Organization of the source code files - right now they are organized
  according to class (e.g. dgeMatrix.R, dgeMatrix.h, dgeMatrix.c).  Is
  there a better way?
  -- This seems ok.

- Fix the calculation of the Dim slot for the crossprod method for
  dgCMatrix objects (too tired to do that now).
  -- Done

- spelling style: Should "coersion" be "coercion" ?
  -- Yes.  Watch for this.

- 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
  --DB - now have both working, I believe.

- man/Matrix.Rd :  has example with dimnames, but we just drop them!
        MM thinks dimnames should be supported (but then ...)
  -- added 'Dimnames' slot (2005-02-10)

- bCrosstab(): yes, we really do want the diagonal "V:V" crosstabs.
   -- explained a bit more in man/bCrosstab.Rd

- Clean up vestigial functions (pdFactor, pdMatrix, matrix<-) from the
  nlme package.

- 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.

- tcrossprod() now works: C code now "exported" via init.c

- Fixed: dtpMatrix(... diag = "U") (i.e., unit-diagonal packed triangular)
         *does* need 'x' entries for the diagonal but these are never looked at.
    -> changed doc -- Lapack also says they are not referenced but assumed 1.


- in lmer.c check all instances of the use of ZtX and XtX and change
  them so that having a negative last element of nc means use the
  response only (but look for it in the right place).

- Solved:

   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}

-  slot "factors" maybe should move up to "Matrix" -- done, 2005-09-28

- arithmetic for sparse matrices:
     done for    <sparseMatrix>  o  <scalar>
  {more needed: see TODO}