output/script/template_function.R

In Chang-Yu-Chang/MigrationCommunity: Microbial Consumer-Resource Model

#' Title of this function
#' @description A short description of the function 
#' @name myfun Name of the function. "Verb" term is preferred.
#' @param par1 Description the first argument. Type of this argument
#' @param par2 The intial (state) values for the ODE. Vector.
#' @return The description of the returned function
#' @examples
#' # Load package and example parameters
#' library(MigrationCommunity)
#' data(example_parameter)
#' 
#' # Do something
#' myfunc(par1, par2)

CR_ode <- function(time, state, parameters){
  with(as.list(c(state, parameters)), {
    # Create a vector of R
    RR <- sapply(paste0('R', sprintf("%03d", re)), function(x) eval(parse(text=x)))
    
    # Create a vector of X
    XX <- sapply(paste0('X', sprintf("%05d", sp)), function(x) eval(parse(text=x)))
    
    # Resource derivatives
    dR <- J * (Rin[re] - RR)
    for (i in 1:length(sp)) dR <- dR + stoi[,,sp[i]] %*% (u[,sp[i]] * RR) * XX[i] # Loop through species
    
    # Consumer derivatives
    dX <- XX * (t(u[,sp] * w[,sp]) %*% RR - J)
    
    # Return dR and dX
    return(list(c(dR,dX)))
  })
}