#' Adding rules
#'
#' This function allows user to define rules. Rules can be used to specify values for model species
#' based on the values of other components (mainly species) in the model. Current version allows only
#' for the ODEs type of rules.
#'
#' @param x model to which the rule is added (required)
#' @param rName - rule name (required)
#' @param type rule type; currently only type ODEs is supported (rules in the form of ODEs) (required)
#' @param rule rule definition (required)
#' @param overwrite a flag that allows changes to the existing rule (default value FALSE)
#'
#' @return This function adds information about rules into the model (given as a first argument of the function).
#' Rules information is stored in the list format and contain the following elements:
#' \itemize{
#' \item{rule$rName - rule name}
#' \item{rule$rType - rule type (ODEs)}
#' \item{rule$rRule - rule definition}
#' }
#'
#' @examples
#' exmp <- newModel("This is an example of a new model")
#' addMAreaction(exmp, react="A = null", "rf", "rb")
#' addMAreaction(exmp, react="A + B -> 2*AB", "k", name="Forward AB")
#' addMAreaction(exmp, react="AB -> null", "rAB")
#'
#' addMAreactRate(exmp, "rf", "fixed", "1")
#' addMAreactRate(exmp, "rb", "fixed", "0.75")
#' addMAreactRate(exmp, "k", "fixed", "0.5")
#' addMAreactRate(exmp, "rAB", "assigned", "p1*A")
#'
#' addParameters(exmp, "p1", 0.75)
#'
#' addSpecies(exmp, "A", 10)
#' addSpecies(exmp, "B", 10)
#' addSpecies(exmp, "AB", 0)
#'
#' addRule(exmp, "rule B", "ODEs", "B=-0.1*AB")
#'
#' # Show info about model reactions and rules
#' exmp$reaction
#' exmp$rule
#'
#' @export
#'
#addRule.function <- function(x, rName=NA, type=NA, rule=NA, overwrite=FALSE){
addRule <- function(x, rName=NA, type=NA, rule=NA, overwrite=FALSE){
if (!exists(deparse(substitute(x))))
stop("Specified model does not exist!")
if (is.na(rName) | is.na(type) | is.na(rule))
stop("Rule name and/or rule and/or type is/are not specified!")
if (!(type %in% c("ODEs")))
stop("Rule type is not in the correct format! Currently, the only supported format is ODEs")
# TDB - expand supported formats
# Algebraic format should suport numerical solution (may not give an exact solution, but approximation)
#if (!(type %in% c("initial", "repeated", "algebraic", "ODEs")))
# stop("Rule type is not in the correct format! Allowed formats are: initial, repeated, algebraic, and ODEs")
y <- x
# Current number of rules
curNumber <- length(y$rules)
# Check if species with the same name exist
if (curNumber > 0){
if (rName %in% y$rules$rName){
print("Rule with the same name already exist in the model!")
if (overwrite){
getIndex <- which(y$rules$rName == rName)
if ((y$rules$rType[getIndex] != type) | (y$rules$rRule[getIndex] != rule)){
y$rules$rType[getIndex] <- type
y$rules$rRule[getIndex] <- rule
print("Rule type and/or rule itself have been replaced")
} else {
print("The new rule and its type are the same as the old ones")
}
} else {
stop("Specify a different rule or set overwrite flag to TRUE!")
}
} else {
y$rules$rName <- c(y$rules$rName, rName)
y$rules$rType <- c(y$rules$rType, type)
y$rules$rRule <- c(y$rules$rRule, rule)
}
} else {
y$rules<- list(rName=rName, rType=type, rRule=rule)
}
y$isChecked <- 0
assign(deparse(substitute(x)), y, envir = .GlobalEnv)
}
#addRule <- cmpfun(addRule.function)
#rm(addRule.function)
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