Nothing
#_______________________________________________________________________________
#---- autoDetectNONMEM ----
#_______________________________________________________________________________
#' Auto-detect special variables from NONMEM as compartment properties.
#' Bioavailabilities, infusion durations/rates and lag times will be automatically
#' detected.
#'
#' @param object object that has NONMEM special variables to be identified
#' @param ... extra arguments, unused
#' @return updated object
#' @export
#' @rdname autoDetectNONMEM
autoDetectNONMEM <- function(object, ...) {
stop("No default function is provided")
}
setGeneric("autoDetectNONMEM", function(object, ...) {
standardGeneric("autoDetectNONMEM")
})
#_______________________________________________________________________________
#---- disable ----
#_______________________________________________________________________________
#' Disable.
#'
#' @param object generic object
#' @param x what needs to be disabled
#' @param ... extra arguments needed for disabling
#' @return object with some disabled features
#' @export
#' @rdname disable
disable <- function(object, x, ...) {
stop("No default function is provided")
}
setGeneric("disable", function(object, x, ...) {
standardGeneric("disable")
})
#_______________________________________________________________________________
#---- export_type ----
#_______________________________________________________________________________
#' Export type class.
#'
#' @export
setClass(
"export_type",
representation(
)
)
#_______________________________________________________________________________
#---- export ----
#_______________________________________________________________________________
#' Export function.
#'
#' @param object generic object
#' @param dest destination
#' @param ... optional arguments
#' @return specific object depending on given destination
#' @export
#' @rdname export
export <- function(object, dest, ...) {
stop("No default function is provided")
}
setGeneric("export", function(object, dest, ...) {
standardGeneric("export")
})
#_______________________________________________________________________________
#---- getCompartmentIndex ----
#_______________________________________________________________________________
#' Get the compartment index for the specified compartment name.
#'
#' @param object generic object that contains compartments information
#' @param name compartment name
#' @return the corresponding compartment index
#' @export
#' @rdname getCompartmentIndex
getCompartmentIndex <- function(object, name) {
stop("No default function is provided")
}
setGeneric("getCompartmentIndex", function(object, name) {
standardGeneric("getCompartmentIndex")
})
#_______________________________________________________________________________
#---- getUncertainty ----
#_______________________________________________________________________________
#' Get uncertainty on the parameters.
#'
#' @param object generic object
#' @param ... extra arguments
#' @return data frame with standard error (se) and relative standard error (rse%) columns
#' @export
#' @rdname getUncertainty
getUncertainty <- function(object, ...) {
stop("No default function is provided")
}
setGeneric("getUncertainty", function(object, ...) {
standardGeneric("getUncertainty")
})
#_______________________________________________________________________________
#---- getVarCov ----
#_______________________________________________________________________________
#' Get variance-covariance matrix.
#'
#' @param object generic object
#' @return a variance-covariance matrix (data frame) or NULL if no matrix present
#' @export
#' @rdname getVarCov
getVarCov <- function(object) {
stop("No default function is provided")
}
setGeneric("getVarCov", function(object) {
standardGeneric("getVarCov")
})
#_______________________________________________________________________________
#---- read ----
#_______________________________________________________________________________
#' Generic read method to read data from a file or a folder.
#'
#' @param file path to the file or folder to be read
#' @param ... extra arguments
#' @return the object representation of the data contained in the file
#' @export
read <- function(file, ...) {
stop("No default function is provided")
}
setGeneric("read", function(file, ...) {
standardGeneric("read")
})
#_______________________________________________________________________________
#---- replaceAll ----
#_______________________________________________________________________________
#' Replace all occurrences in object.
#'
#' @param object generic object (e.g. model, code_record(s), etc.)
#' @param pattern pattern to be replaced
#' @param replacement replacement string
#' @param ... extra arguments
#' @return the same object with all occurrences replaced
#' @export
replaceAll <- function(object, pattern, replacement, ...) {
stop("No default function is provided")
}
setGeneric("replaceAll", function(object, pattern, replacement, ...) {
standardGeneric("replaceAll")
})
#_______________________________________________________________________________
#---- select ----
#_______________________________________________________________________________
#' Get a subset of an object.
#'
#' @param object generic object
#' @param ... arguments to select
#' @return subset of an object
#' @export
#' @rdname select
select <- function(object, ...) {
stop("No default function is provided")
}
setGeneric("select", function(object, ...) {
standardGeneric("select")
})
#' @rdname select
setMethod("select", signature=c("data.frame"), definition=function(object, ...) {
return(return(dplyr::select(.data=object, ...)))
})
#_______________________________________________________________________________
#---- standardise ----
#_______________________________________________________________________________
#' Standardise.
#'
#' @param object generic object
#' @param ... extra arguments needed for standardisation
#' @return standardised object
#' @export
#' @rdname standardise
standardise <- function(object, ...) {
stop("No default function is provided")
}
setGeneric("standardise", function(object, ...) {
standardGeneric("standardise")
})
#_______________________________________________________________________________
#---- toString ----
#_______________________________________________________________________________
#' ToString generic method.
#'
#' @param object generic object
#' @param ... extra arguments needed for toString conversion
#' @return character value/vector
#' @export
#' @rdname toString
toString <- function(object, ...) {
stop("No default function is provided")
}
setGeneric("toString", function(object, ...) {
standardGeneric("toString")
})
#_______________________________________________________________________________
#---- write ----
#_______________________________________________________________________________
#' Write generic object to files.
#'
#' @param object generic object
#' @param file path of the output file or directory
#' @param ... extra arguments
#' @return logical value, TRUE for success, FALSE for failure
#' @export
#' @rdname write
write <- function(object, file, ...) {
stop("No default function is provided")
}
setGeneric("write", function(object, file, ...) {
standardGeneric("write")
})
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