#' Adding species
#'
#' This function allows users to specify initial values for species within the model.
#' Model must contain at least one species. Initial values for all species, as well as all rates and
#' parameters have to be defined. sysBio uses a term null to describe a null species (source or sink);
#' null species do not need to be defined.
#'
#' @param x model to which the species is added (required)
#' @param spName species name (required)
#' @param iVal initial value; if the value is not specified, sysBio will set initial value to 0
#' @param overwrite a flag that allows changes to the existing species (default value FALSE)
#'
#' @return This function adds information about species into the model (given as a first argument of the function).
#' Species information is stored in the list format and contain the following elements:
#' \itemize{
#' \item{species$sName - species name}
#' \item{species$initVal - initial value}
#' }
#'
#' @examples
#' exmp <- newModel("This is an example of a new model")
#' addMAreaction(exmp, react="A = null", "rf", "rb")
#' addMAreaction(exmp, react="A + B -> 2*AB", "k", name="Forward AB")
#' addMAreaction(exmp, react="AB -> null", "rAB")
#'
#' addMAreactRate(exmp, "rf", "fixed", "1")
#' addMAreactRate(exmp, "rb", "fixed", "0.75")
#' addMAreactRate(exmp, "k", "fixed", "0.5")
#' addMAreactRate(exmp, "rAB", "assigned", "p1*A")
#'
#' addParameters(exmp, "p1", 0.75)
#'
#' addSpecies(exmp, "A", 10)
#' addSpecies(exmp, "B", 10)
#' addSpecies(exmp, "AB", 0)
#'
#' # Show info about model reactions and species
#' exmp$reaction
#' exmp$species
#'
#' @export
#'
#addSpecies.function <- function(x, spName=NA, iVal="0", overwrite=FALSE){
addSpecies <- function(x, spName=NA, iVal="0", overwrite=FALSE){
if (!exists(deparse(substitute(x))))
stop("Specified model does not exist!")
if (is.na(spName))
stop("Species name is not specified!")
y <- x
# Current number of species
curNumber <- length(y$species)
# Check if species with the same name exist
if (curNumber > 0){
if (spName %in% y$species$sName){
print("Species with the same name already exist in the model!")
if (overwrite){
getIndex <- which(y$species$sName == spName)
if (y$species$initVal[getIndex] != iVal){
y$species$initVal[getIndex] <- iVal
print("Initial value has been replaced")
} else {
print("The new initial value is the same as the old one")
}
} else {
stop("Specify a different species or set overwrite flag to TRUE!")
}
} else {
y$species$sName <- c(y$species$sName, spName)
y$species$initVal <- c(y$species$initVal, iVal)
}
} else {
y$species <- list(sName=spName, initVal=iVal)
}
y$isChecked <- 0
assign(deparse(substitute(x)), y, envir = .GlobalEnv)
}
#addSpecies <- cmpfun(addSpecies.function)
#rm(addSpecies.function)
Add the following code to your website.
For more information on customizing the embed code, read Embedding Snippets.