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**1329**- (**download**) (**annotate**)*Fri Jul 21 06:47:06 2006 UTC*(13 years, 8 months ago) by*maechler*File size: 4504 byte(s)

miscellaneous mostly related to sparse indexing

----- 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? ----- Check for DimNames propagation in coercion and other operations. ----- - 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. ------ - 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 ------- - 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*) --- - 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). --- - "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

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