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Revision 1150 - (download) (annotate)
Thu Jan 12 03:41:25 2006 UTC (13 years, 10 months ago) by bates
File size: 3803 byte(s)
Switch to supernodal Cholesky representation of mer objects
useDynLib(Matrix, .registration=TRUE)

importFrom("graphics",image)
#importFrom("graphics",plot)		## lmer-related
importFrom("lattice", levelplot)
importFrom("grid",    grid.rect, gpar, grob)
import("stats")				## lmer-related

## Currently, group generics need to be explicitly imported (Bug?):
importFrom("methods", Arith, Compare, Math, Math2, Summary, Complex)

## Generics and functions defined in this package
export("Diagonal",
       "Hilbert",
       "Matrix",
       "Schur",
       "expand",
       "expm",
       "facmul",
       #not yet on purpose: "isSymmetric",
       "lu",
       "norm",
       "rcond",
       "readHB",
       "readMM",
       "tcrossprod",
       "unpack",
       "writeHB",
       "writeMM"
       )

## workaround S4-Group(generic|method) quirk: R/AllGeneric.R
## needs setGeneric(*, group=) and this for all non-Primitives :
export(
       ## "Math"
       "log",
       "gamma",
       "lgamma",

       ## "Math2"
       "round",
       "signif",

       ## "Summary"
       "max",
       "min",
       "range",
       "prod",
       "sum",
       "any",
       "all"
)


## lmer-related
export("lmer", "mcmcsamp")

exportClasses(
	      "index",

	      "BunchKaufman",
	      "pBunchKaufman",
	      "Cholesky",
	      "pCholesky",
	      "LU",
	      "Matrix",
	      ## also intermediate `virtual' ones:
	      "dMatrix",
	      "lMatrix",
	      "denseMatrix",
	      "sparseMatrix",
              "symmetricMatrix",
              "triangularMatrix",
              "diagonalMatrix",
	      "dsparseMatrix",
	      "lsparseMatrix",
	      "TsparseMatrix",
	      "CsparseMatrix",
	      "ddenseMatrix",
	      ## not yet used, but as sub-classes;
	      ## need to provide them for 'hierarchy-analysis':
	      "iMatrix",
	      "zMatrix",
	      "ldenseMatrix",

	      "dgCMatrix",
	      "dgRMatrix",# unused
	      "dgTMatrix",
	      "dgeMatrix",
	      "dpoMatrix",
	      "dppMatrix",
	      "dsCMatrix",
	      "dsRMatrix",# unused
	      "dsTMatrix",
	      "dspMatrix",
	      "dsyMatrix",
	      "dtCMatrix",
	      "dtRMatrix",# unused
	      "dtTMatrix",
	      "dtpMatrix",
	      "dtrMatrix",
              "ddiMatrix",

	      "lgeMatrix",
	      "lspMatrix",
	      "lsyMatrix",
	      "ltpMatrix",
	      "ltrMatrix",
              "ldiMatrix",

	      "lgCMatrix",
	      "lgRMatrix",
	      "lgTMatrix",
	      "lsCMatrix",
	      "lsRMatrix",# unused
	      "lsTMatrix",
	      "ltCMatrix",
	      "ltRMatrix",# unused
	      "ltTMatrix",
              "pMatrix",
              
	      "dCholCMatrix",
	      "lCholCMatrix",
              "dCHMsuper",
              "dCHMsimpl"
              # "correlation" # unused
	      )

## lmer-related
exportClasses("lmer", "mer")


exportMethods(
	      ## Group Methods
	      "Arith",
	      "Math",
	      "Math2",
	      "Summary",
	      "Compare",

	      "!",
	      "+",# for dgT(Matrix) only
	      "%*%",

	      "Schur",
	      "as.array",
	      "as.matrix",
	      "as.vector",
	      "chol",
	      "colMeans",
	      "colSums",
	      "coerce",
	      "crossprod",
	      "determinant",
	      "diag",
	      "dim",
	      "dimnames",
	      "dimnames<-",
	      "expand",
	      "expm",
	      "kronecker",
	      "image",
	      "norm",
	      "rcond",
	      "rowMeans",
	      "rowSums",
	      "show",
	      "solve",
	      "t",
	      "tcrossprod"
	      )

## only for R >= 2.2:
if(paste(R.version$major, R.version$minor, sep=".") >= "2.2") {

exportMethods("rbind2")
exportMethods("cbind2")

}


## lmer-related
exportMethods("BIC", "anova", "coef", "confint", "deviance", "fitted",
	      "fixef", "formula", "lmer", "logLik", "mcmcsamp",
	      # "plot",
              "ranef", "residuals", "resid", "simulate",
	      "summary", "update", "vcov", "VarCorr", "with")


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