The R Project SVN R-packages

#### Define those generics that we need, if they don't exist;
#### not all will be exported

if (!isGeneric("expand"))
    setGeneric("expand", function(x, ...) standardGeneric("expand"))

## if (!isGeneric("tcrossprod"))
##   setGeneric("tcrossprod", function(x, y = NULL) standardGeneric("tcrossprod"))
if (!exists("tcrossprod"))# R <= 2.2.x :
    tcrossprod <- function(x, y = NULL) x %*% t(if(is.null(y)) x else y)
## will become generic by setMethod(..)

if (!isGeneric("isDiagonal"))
    setGeneric("isDiagonal", function(object, ...)
               standardGeneric("isDiagonal"))

if (!isGeneric("isSymmetric"))
    ## no "..." here at the moment; must match isSymmetric()
    ## R 2.3.x base/R/eigen.R
    setGeneric("isSymmetric", function(object, ...)# no 'tol' in generic
           standardGeneric("isSymmetric"))

if (!isGeneric("isTriangular"))
    setGeneric("isTriangular", function(object, ...)
               standardGeneric("isTriangular"))

if (!isGeneric("isNested"))
    setGeneric("isNested", function(object, ...) standardGeneric("isNested"))

if (!isGeneric("facmul"))
    setGeneric("facmul",
               function(x, factor, y, transpose, left, ...)
               standardGeneric("facmul"))

if (!isGeneric("lu"))
    setGeneric("lu", function(x, ...) standardGeneric("lu"))

if (!isGeneric("norm"))
    setGeneric("norm", function(x, type, ...) standardGeneric("norm"))

if (!isGeneric("rcond"))
    setGeneric("rcond", function(x, type, ...) standardGeneric("rcond"))

if (!isGeneric("Schur"))
    setGeneric("Schur", function(x, vectors, ...) standardGeneric("Schur"))

if (!isGeneric("unpack"))
    setGeneric("unpack", function(x, ...) standardGeneric("unpack"))

##- if (!isGeneric("%p%"))
##-     setGeneric("%p%", function(a, b) standardGeneric("%p%"))

if (!isGeneric("expm"))
    setGeneric("expm", function(x) standardGeneric("expm"))

if (!isGeneric("writeHB"))
    setGeneric("writeHB", function(obj, file, ...)
               standardGeneric("writeHB"))

if (!isGeneric("writeMM"))
    setGeneric("writeMM", function(obj, file, ...)
               standardGeneric("writeMM"))

## ----------------------- lmer-related Generics ---------------------------

## Hmm: If this does not match *exactly* the "formula" - method in ./lmer.R
## ---  the  match.call() in there may give a very different result
setGeneric("lmer",
           function(formula, data, family,
                    method = c("REML", "ML", "PQL", "Laplace", "AGQ"),
                    control = list(), start, subset, weights, na.action,
                    offset, model = TRUE, x = FALSE, y = FALSE,
                    ...)
           standardGeneric("lmer"))


if (!isGeneric("LMEoptimize<-")) {
    setGeneric("LMEoptimize<-", function(x, ..., value)
               standardGeneric("LMEoptimize<-"))
}

if (!isGeneric("fixef")) {
    setGeneric("fixef", function(object, ...) standardGeneric("fixef"))
}

fixed.effects <- function(object, ...) {
    ## fixed.effects was an alternative name for fixef
    .Deprecated("fixef")
    mCall = match.call()
    mCall[[1]] = as.name("fixef")
    eval(mCall, parent.frame())
}

if (!isGeneric("ranef")) {
    setGeneric("ranef", function(object, ...)
               standardGeneric("ranef"))
}

random.effects <- function(object, ...) {
    ## random.effects was an alternative name for ranef
    .Deprecated("ranef")
    mCall = match.call()
    mCall[[1]] = as.name("ranef")
    eval(mCall, parent.frame())
}

if (!isGeneric("BIC")) {
    setGeneric("BIC", function(object, ...) standardGeneric("BIC"))
}

setMethod("BIC", "logLik",
          function(object, ...)
          -2 * (c(object) - attr(object, "df") * log(attr(object, "nobs"))/2)
          )

if (!isGeneric("VarCorr")) {
    setGeneric("VarCorr", function(x, ...) standardGeneric("VarCorr"))
}

if (!isGeneric("gradient")) {           # not exported
    setGeneric("gradient", function(x, ...) standardGeneric("gradient"))
}

if (!isGeneric("getFixDF")) {           # not exported
    setGeneric("getFixDF", function(object, ...) standardGeneric("getFixDF"))
}

if (!isGeneric("mcmcsamp")) {
    setGeneric("mcmcsamp", function(object, n = 1, verbose =
    FALSE, ...) standardGeneric("mcmcsamp"))
}

if (!exists("simulate", mode = "function")) {
    setGeneric("simulate", function(object, nsim = 1, seed = NULL, ...)
               standardGeneric("simulate"))
}

###---- Group Generics ----
## The following are **WORKAROUND** s currently needed for all non-Primitives:

##  "Math"
setGeneric("log", group="Math")
setGeneric("gamma", group="Math")
setGeneric("lgamma", group="Math")

## "Math2"
setGeneric("round",  group="Math2")
setGeneric("signif", group="Math2")

## "Summary" --- this needs some hoop jumping that may become unnecessary
##               in a future version of R (>= 2.3.x):

.max_def <- function(x, ..., na.rm = FALSE) base::max(x, ..., na.rm = na.rm)
.min_def <- function(x, ..., na.rm = FALSE) base::min(x, ..., na.rm = na.rm)
.range_def <- function(x, ..., na.rm = FALSE) base::range(x, ..., na.rm = na.rm)
.prod_def <- function(x, ..., na.rm = FALSE) base::prod(x, ..., na.rm = na.rm)
.sum_def <- function(x, ..., na.rm = FALSE) base::sum(x, ..., na.rm = na.rm)
.any_def <- function(x, ..., na.rm = FALSE) base::any(x, ..., na.rm = na.rm)
.all_def <- function(x, ..., na.rm = FALSE) base::all(x, ..., na.rm = na.rm)

setGeneric("max", function(x, ..., na.rm = FALSE) standardGeneric("max"),
           useAsDefault = .max_def, group = "Summary")
setGeneric("min", function(x, ..., na.rm = FALSE) standardGeneric("min"),
           useAsDefault = .min_def, group="Summary")
setGeneric("range", function(x, ..., na.rm = FALSE) standardGeneric("range"),
           useAsDefault = .range_def, group="Summary")
setGeneric("prod", function(x, ..., na.rm = FALSE) standardGeneric("prod"),
           useAsDefault = .prod_def, group="Summary")
setGeneric("sum", function(x, ..., na.rm = FALSE) standardGeneric("sum"),
           useAsDefault = .sum_def, group="Summary")
setGeneric("any", function(x, ..., na.rm = FALSE) standardGeneric("any"),
           useAsDefault = .any_def, group="Summary")
setGeneric("all", function(x, ..., na.rm = FALSE) standardGeneric("all"),
           useAsDefault = .all_def, group="Summary")