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Revision 2586 - (download) (annotate)
Sun Jul 25 02:32:06 2010 UTC (9 years, 4 months ago) by mmaechler
File size: 7606 byte(s)
move Matrix/ directory "down"
useDynLib(Matrix, .registration=TRUE)

## Import non-base functions we need explicitly,
## notably for which we define methods:
importFrom("lattice", levelplot)
importFrom("graphics", image)
importFrom("utils", head, tail)
importFrom("stats", ## potentially all these (we import into 'lme4a'):
           # anova,
           coef,# confint,
           cov2cor,# deviance,
           fitted,
           formula,# predict, profile,
           residuals,# simulate, terms,
           update#, vcov
           )

importFrom("grid", grid.rect, gpar, grob)# others via 'grid::'

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

## Generics and functions defined in this package
export("Cholesky",
       "Diagonal", ".symDiagonal", ".sparseDiagonal",
       "Hilbert",
       "Matrix",
       "spMatrix",
       "sparseMatrix",
       "Schur",
       "abIseq", "abIseq1", "rep2abI",
       "band",
       "bandSparse",
       "bdiag",
## no longer; implicit generics now
       ## "colMeans", "colSums", ## these needed a "..." added
       ## "rowMeans", "rowSums",
       "condest", "onenormest",
       "det",# << "identical" as base - but with correct determinant()
       "drop0",
       "expand",
       "expm",
       "facmul",
       "forceSymmetric",
       "getCall",
#	 "isTriangular",
#	 "isDiagonal",
       "isLDL",
#TODO       "lm.fit.sparse",# <- "somewhat experimental"
       "lu",
       "mkRespMod",
       "model.Matrix",
       "nearPD",
       "nnzero",
       "printSpMatrix",
       "printSpMatrix2",
       "rankMatrix",
       "readHB",
       "readMM",
       "sparse.model.matrix",
       "symmpart",
       "skewpart",
       "tcrossprod",
       "tril",
       "triu",
       "unpack"
       , ".validateCsparse"
#        "writeHB",
       , "writeMM"
       , ".M.classEnv"
       )

## substitute for using  cbind() / rbind()
export("cBind",
       "rBind")


exportClasses(
              ## Class unions:
	      "index",
	      "replValue", # if we don't export it, things fail in dispatch
	      "atomicVector",
	      "number",
## LOGIC      "logic",
              "abIndex", "rleDiff",

	      ## --- 'Matrix' mother and all its daughters : ---------------
	      "Matrix",
	      ## also intermediate `virtual' ones:
	      "dMatrix",
	      "lMatrix",
	      "nMatrix",
	      ## not yet used, but as sub-classes;
	      ## must provide them for 'hierarchy-analysis':
	      "iMatrix",
	      "zMatrix",

	      "denseMatrix",
	      "sparseMatrix",

	      "compMatrix",
	      "diagonalMatrix",
	      "generalMatrix",
	      "symmetricMatrix",
	      "triangularMatrix",

	      "dsparseMatrix",
	      "lsparseMatrix",
	      "nsparseMatrix",
	      "TsparseMatrix",
	      "CsparseMatrix",
	      "RsparseMatrix",
	      "ddenseMatrix",
	      "ldenseMatrix",
	      "ndenseMatrix",

	      "dgCMatrix",
	      "dgRMatrix",
	      "dgTMatrix",
	      "dgeMatrix",
	      "dpoMatrix",
	      "dppMatrix",
	      "dsCMatrix",
	      "dsRMatrix",
	      "dsTMatrix",
	      "dspMatrix",
	      "dsyMatrix",
	      "dtCMatrix",
	      "dtRMatrix",
	      "dtTMatrix",
	      "dtpMatrix",
	      "dtrMatrix",
	      "ddiMatrix",
	      "lgeMatrix",
	      "lspMatrix",
	      "lsyMatrix",
	      "ltpMatrix",
	      "ltrMatrix",
	      "ldiMatrix",
	      "ngeMatrix",
	      "nspMatrix",
	      "nsyMatrix",
	      "ntpMatrix",
	      "ntrMatrix",

	      "lgCMatrix",
	      "lgRMatrix",
	      "lgTMatrix",
	      "lsCMatrix",
	      "lsRMatrix",
	      "lsTMatrix",
	      "ltCMatrix",
	      "ltRMatrix",
	      "ltTMatrix",

	      "ngCMatrix",
	      "ngRMatrix",
	      "ngTMatrix",
	      "nsCMatrix",
	      "nsRMatrix",
	      "nsTMatrix",
	      "ntCMatrix",
	      "ntRMatrix",
	      "ntTMatrix",

	      "pMatrix",

	      "corMatrix", # unused

              ##
              "modelMatrix",
              "sparseModelMatrix",
              "denseModelMatrix",
              "dsparseModelMatrix",
              "ddenseModelMatrix",

	      ## --- inheriting "Matrix", but also factorizations:
	      "BunchKaufman",
	      "pBunchKaufman",
	      "Cholesky",
	      "pCholesky",
	      ## "LDL",

	      ## --- 'MatrixFactorization' mother and all its daughters : ---

	      "MatrixFactorization",
	      "CholeskyFactorization",

	      "LU",
	      "denseLU",
	      "sparseLU",

	      "CHMfactor",
	      "CHMsuper",
	      "CHMsimpl",
	      "dCHMsuper",
	      "dCHMsimpl",
	      "nCHMsuper",# unused
	      "nCHMsimpl",# unused

	      "sparseQR",
## 	      "SPQR",

	      "Schur",

	      "sparseVector", ## --- and daughters : ---
	      "dsparseVector",
	      "isparseVector",
	      "lsparseVector",
	      "nsparseVector",
	      "zsparseVector",
	      "xsparseVector", # the class union of all 'x' lost sparseVector's

              ## --- linear predictor modules, containing a model matrix
              "predModule",
              "dPredModule",# dense &
              "sPredModule",# sparse  (for now)

              ## --- response modules, containing a response vector, etc.
              "respModule",          # base class and also linear model
              "glmRespMod",          # generalized linear models
              "nlsRespMod",          # nonlinear regression response
              "nglmRespMod",         # generalized nonlinear

              "glpModel", "Model"
	      )



exportMethods(## for both own and "other" generics:

	      ## Group Methods
	      "Arith",
	      "Compare",
	      "Logic",
	      "Math",
	      "Math2",
	      "Ops",
	      "Summary",

              ## re-export S4 methods, for "stats"-S3-generics:
              "coef", "cov2cor",
              "fitted", "formula", "residuals",
              "update",


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

	      "all",
	      "any",
	      "all.equal",

	      "BunchKaufman",
	      "Cholesky",
	      "Schur",
	      "as.array",
	      "as.matrix",
	      "as.vector",
	      "as.numeric",
	      "as.integer",
	      "as.logical",
	      "band",
	      "chol",
              "chol2inv",
	      "colMeans",
	      "colSums",
	      "coerce",
	      "crossprod",
	      "determinant",
	      "diag",
	      "diff",
	      "dim",
	      "dim<-",
	      "dimnames",
	      "dimnames<-",
              "drop",
	      "expand",
	      "expm",
	      "getCall",
	      "head",
	      "image",
	      "forceSymmetric",
	      "isSymmetric",
##	       "isDiagonal",
##	       "isTriangular",
              "is.na",
	      "kronecker",
	      "length",
              "mean",
	      "norm",
              "nnzero",
              "print",# print(x, ...) when show(x) is not sufficient
	      "qr",
	      "qr.R",
	      "qr.qy",
	      "qr.qty",
	      "qr.coef",
	      "qr.resid",
	      "qr.fitted",
	      "rep",
	      "rcond",
	      "rowMeans",
	      "rowSums",
	      "show",
	      "solve",
##               "spqr",
	      "summary",
              "symmpart",
              "skewpart",
	      "t",
	      "tail",
	      "tcrossprod",
	      "tril",
	      "triu",
              "unname",
              "which",
	      "zapsmall"
	      )

if(getRversion() < "2.10.0")# The version of R -- at *install* time (!)
    exportPattern("^contr\\..*")

if(getRversion() < "2.10.0")
    export("xtabs")

if(getRversion() < "2.11.0" || R.version$`svn rev` < 51018)
    export("norm")

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

S3method(print, sparseSummary)
S3method(c, abIndex)# < for now -- S4 method on c() seems "difficult"

root@r-forge.r-project.org
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