path: root/R/mkinsub.R

#' Function to set up a kinetic submodel for one state variable
#' 
#' This is a convenience function to set up the lists used as arguments for
#' \code{\link{mkinmod}}.
#' 
#' @param submodel Character vector of length one to specify the submodel type.
#'   See \code{\link{mkinmod}} for the list of allowed submodel names.
#' @param to Vector of the names of the state variable to which a
#'   transformation shall be included in the model.
#' @param sink Should a pathway to sink be included in the model in addition to
#'   the pathways to other state variables?
#' @param full_name An optional name to be used e.g. for plotting fits
#'   performed with the model.  You can use non-ASCII characters here, but then
#'   your R code will not be portable, \emph{i.e.} may produce unintended plot
#'   results on other operating systems or system configurations.
#' @return A list for use with \code{\link{mkinmod}}.
#' @author Johannes Ranke
#' @examples
#' 
#' # One parent compound, one metabolite, both single first order.
#' SFO_SFO <- mkinmod(
#'   parent = list(type = "SFO", to = "m1"),
#'   m1 = list(type = "SFO"))
#' 
#' # The same model using mkinsub
#' SFO_SFO.2 <- mkinmod(
#'   parent = mkinsub("SFO", "m1"),
#'   m1 = mkinsub("SFO"))
#' 
#' \dontrun{
#'   # Now supplying full names
#'   SFO_SFO.2 <- mkinmod(
#'     parent = mkinsub("SFO", "m1", full_name = "Test compound"),
#'     m1 = mkinsub("SFO", full_name = "Metabolite M1"))
#'  }
#' @export
mkinsub <- function(submodel, to = NULL, sink = TRUE, full_name = NA)
{
  return(list(type = submodel, to = to, sink = sink, full_name = full_name))
}