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- Sparse matrix methods can now be based on the CHOLMOD package.  We
   will need to migrate from the current code to CHOLMOD-based code
   using #ifdef USE_CHOLMOD.  Some of the things to be done

   - Move documentation from subdirectories of src to inst/doc

   - Write utilities to create a cholmod_sparse pointer from a
   dgCMatrix or lgCMatrix (or zgCMatrix) object without copying and
   allocating.

   - Start adding simple S4 methods ( %*%, +, cbind, t) for
     CsparseMatrix using CHOLMOD.

- 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

- group generics: "Arith", also "Compare", "Math" etc;
  see ?Math  and the examples in ?SetGeneric

- methods for rbind and cbind where they make sense:
  R 2.2.0 (and newer) provide cbind2() and rbind2() generics and default
  methods [following John Chambers's proposition], and we have implemented
  methods for them.

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

- rcond() of a singular dpoMatrix gives a LaPack error instead of just 0:
  MM <- crossprod(M <- Matrix(c(1:4,9:6), 2,4)) ; rcond(MM)
  Done(2005-10-03): The error message is more helpful now.

- implement diagonal Matrix class  "ddiMatrix" etc
  using constructor function Diagonal() {and extractor diag()}.
  Done(2006-01-03)

- new("ltTMatrix") now at least prints

-- Done by version 0.995-1 ---


- Migration of lmer from the mer representation to the mer2
   representation and the use of the CHOLMOD code for the sparse
   matrix decomposition.  Some of the things that need to be done.

   - Matrices in the mer2 representation are classed matrices, in the
   mer representation they were unclassed.  Any parts inside the C
   code that would access, for example,
    REAL(GET_SLOT(x, Matrix_RXXSym))
   need to be modified to access
    REAL(GET_SLOT(GET_SLOT(x, Matrix_RXXSym), Matrix_xSym))
   This is especially important for Omega but I think I have done
   those changes already.

   - The components named *X* in an mer object refers to an augmented
   design matrix of p+1 columns.  In the mer2 object there are
   separate slots for rZy and rXy.  The scalar y'y is the first
   element of devComp.

   - Presently nc is of length nf+1 and the last element is n, the
   number of observations.  This value should be moved to devComp and
   nc made of length nf.

   - The slot L is a list of length 1 that contains an ExternalPointer
   to a cholmod_factor object.  This contains a permutation which is
   most easily accessible through cholmod_solve(CHOLMOD_P,...) or
   cholmod_solve(CHOLMOD_Pt,...).  The ZtX, Zty, RZX and rZy slots actually
   contain P%*%RZX and P%*%rZy

- "[<-"  Methods for dgC*  and  dgT* the former building on the latter
     using   j = .Call("Matrix_expand_pointers", x@p, PACKAGE = "Matrix")
     where needed

- Put the matrix 'mm' and the response vector 'y' into 'KNex', a list.
  Modified all examples and tests that used them and the Comparisons vignette.

- rowSums(), colSums(), rowMeans & colMeans() now should work for all
  sparse and dense matrices, via "dgeMatrix", "dgC*" and "dgT*".

- Suitably adjust classes of matrices after subscripting.
  head(Hilbert(9)) and the equivalent expression Hilbert(9)[1:4,]
  now work and return "dgeMatrix" (and not ..symmetric..).

  We try to propagate the class to the subscripted matrix
  but, if that fails its test, fall back on a general matrix class. -- for dense
  That is, the fallback class for dsyMatrix, etc. is dgeMatrix; the
  fallback class for dsCMatrix is dgCMatrix, etc.

- tril(), triu()  now return matrices of *triangular* classes.

- Factorizations: LU and solve() for  *sparse*  Matrices is now done,
  -----------------  using CSparse (and not UMFPACK as originally thought)

- M[i,j] <- "sub-Matrix"  now works.

- "Compare" for dgC & dgT  --- to be able to do  M[M > 10]  etc

-  new("ltTMatrix", diag = "U", Dim = c(2:2, 2:2))   now works

- Diagonal(3) - toeplitz(c(0,1,0))  or
  Diagonal(4) >= 0          now work

- .Call(Csparse_Csparse_crossprod, ...)  for crossprod(x,y) {2-args}

- When 'x' is a symmetric matrix,
  a)  x[i,i] should return a *symmetric* matrix too (when 'i' has length > 1)
  b)  x[i,i] <- scalar_value  should ``keep x symmetric'',
      i.e. also return symmetricM*

- Fully implement "Logic" methods - now (R 2.4.1) that the group is in S4