#' Adding reaction rates
#'
#' This function allows users to define reaction rate. Reaction rate can be
#' defined as a fixed numerical value (e.g., r=m1, where m1 represents a
#' constant parameter, m1=0.9, or just as r=0.9) or initial assignments
#' (e.g., r=m1*A, where m1 represents a constant parameter and A represents
#' a species).
#'
#' @param x model to which the reaction rate is added (required)
#' @param rr reaction rate name (required),
#' @param type reaction rate type; currently supported options are fixed and assigned;
#' if the value is not specified, sysBio will set type to fixed
#' @param val reaction rate value; if defined as fixed, the value should be specified as a number.
#' e.g., 0.1; if defined as assigned, the value can be defined in form of an assignment (function),
#' e.g., B or 10*A. If the value is not specified, sysBio will set the value to 1
#' @param overwrite a flag that allows changes to the existing reaction rate (default value FALSE)
#'
#' @return This function adds information about reaction rates into the model (given as a first argument of the function).
#' Reaction rates information is stored in the list format and contain the following elements:
#' \itemize{
#' \item{rates$rrName - reaction rate name}
#' \item{rates$rType - reaction rate type}
#' \item{rates$rVal - reaction rate value}
#' }
#'
#' @examples
#' exmp <- newModel("This is an example of a new model")
#' addMAreaction(exmp, react="A = null", "rf", "rb")
#' addMAreaction(exmp, react="A + B -> 2*AB", "k", name="Forward AB")
#' addMAreaction(exmp, react="AB -> null", "rAB")
#'
#' addMAreactRate(exmp, "rf", "fixed", "1")
#' addMAreactRate(exmp, "rb", "fixed", "0.75")
#' addMAreactRate(exmp, "k", "fixed", "0.5")
#' addMAreactRate(exmp, "rAB", "assigned", "p1*A")
#'
#'
#' # Show info about model reactions and rates
#' exmp$reaction
#' exmp$rates
#'
#' @export
#'
#addMAreactRate.function <- function(x, rr=NA, type="fixed", val="1", overwrite=FALSE){
addMAreactRate <- function(x, rr=NA, type="fixed", val="1", overwrite=FALSE){
if (!exists(deparse(substitute(x))))
stop("Specified model does not exist!")
if (is.na(rr))
stop("Reaction rate is not specified!")
if (!(type %in% c("fixed", "assigned")))
stop("Reaction type is not in the correct format!")
# Add option to use odes
y <- x
# Current number of species
curNumber <- length(y$rates)
# Check if a reaction rate with the same name exist
if (curNumber > 0){
if (rr %in% y$rates$rrName){
print("Rate with the same name already exist in the model!")
if (overwrite){
getIndex <- which(y$rates$rrName == rr)
if ((y$rates$rType[getIndex] != type) | (y$rates$rVal[getIndex] != val)){
y$rates$rType[getIndex] <- type
y$rates$rVal[getIndex] <- val
print("Initial value and/or type of the reaction have been replaced")
} else {
print("The new initial value and/or type of the reaction are the same as the old one")
}
} else {
stop("Specify a different reaction name or set overwrite flag to TRUE!")
}
} else {
y$rates$rrName <- c(y$rates$rrName, rr)
y$rates$rType <- c(y$rates$rType, type)
y$rates$rVal <- c(y$rates$rVal, val)
}
} else {
y$rates <- list(rrName=rr, rType=type, rVal=val)
}
y$isChecked <- 0
assign(deparse(substitute(x)), y, envir = .GlobalEnv)
}
#addMAreactRate <- cmpfun(addMAreactRate.function)
#rm(addMAreactRate.function)
Add the following code to your website.
For more information on customizing the embed code, read Embedding Snippets.