The R Project SVN R-packages

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Modify mcmcsamp to return the deviance in the sample only when the
optional argument 'deviance' is TRUE (default FALSE).
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Replace the use of the unexported replacement function LMEoptimize<-
in lmer.R by the function LMEopt, which always returns NULL but
(in contradiction to the language specification) modifies its first argument.
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Modify the one-argument form of the anova method for lmer objects (yet
  again) to calculate the F ratios.  It is the df, not the ratio that
  is controversial.
Should there be an extractor function for the mean square error?  If
  so, what should it be called?
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Check for DimNames propagation in coercion and other operations.
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- Revive the "lmer" and "glmer" classes.  Slots like "family" should
  be in "glmer" only.  Many methods for "lmer" can be simplified as,
  for example, they will always use the scale factor.

- Add a "pedigree" class and methods for it.  Allow a pedigree
  argument in lmer.

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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 (rcond, %*%, +, cbind, t).

- Report the problem in the Linux ldexp manual page.  The second and
  third calls in the Synopsis should be to ldexpf and ldexpl.

- [,] indexing: for sparse "works", but not yet for negative indices!

- consider moving alloc3Darray from ./src/Mutils.c to
  $(RSRC)/src/base/array.c

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- 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!

  (have some dtr* <-> dtp*)

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- 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:
         <sparseMatrix>  o  <same-dim-sparseMatrix>
  should return a sparse matrix  for at least "+" and "*" , also %%,
  and "/" and "%/%" at least when the RHS is non-zero a scalar.
  Challenge: nice implementation (``common non-0''; but Tsparse* is not uniq).

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- "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"
  [2005-12-xx: done for dgeMatrix at least]

- "ltTmatrix" :
  2) new("ltTMatrix", diag = "U", Dim = c(2:2, 2:2)) shows lack of ltTM*_validate

- 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"

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

- 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 [ -> solve() ] and Schur()  for  *sparse*  Matrices.
  -----------------  LU-sparse is the purpose of all of ./src/UMFPACK/
    -->  ./inst/doc/UFsparse/*
  Note that UMFPACK is a bit slow compared to TAUCS etc, according to
  Gould et al.(2005)
  And then, possibly eigen(), svd(), qr(), ... for sparse
  {probably base some on the fast  chol() of CHOLMOD}.
  ./man/lu.Rd notes that lu() is not yet available for sparse

  2006-04-15 : now with 'CSparse' { src/cs.c }, have at least solve( <dtC*> )

- nicer pedigree examples and tests

- band(), triu(), tril() for *all*, not just sparse matrices