R/Mussel_pop_main.R

In RAC: R Package for Aqua Culture

#' Mussel bioenergetic population model
#'
#' Solves the bioenergetic balance for Mussel and simulates a population
#'
#' @param userpath the path where the working folder is located
#' @param forcings a list containing the time series in the odd positions and realted forcings in the even positions. Forcings returned are: Water temperature [Celsius degrees], Chlorophyll a concentration [mgChl-a/m^3], particulated organic carbon (POC) concentration [mgC/l] and its characterization in terms of C/P and N/P molar ratios, particulated organic matter (POM) concentration [mgC/l], total suspended solids (TSS) concentration [mg/l]
#' @return A list containing model outputs: weight, length mussel CNP, pseudofecies CNP production, temperature limitation functions, metabolic rates and oxygen consumption
#' @export
#'
#' @import matrixStats plotrix rstudioapi
#'
#' @import grDevices graphics utils stats
#'

Mussel_pop_main<-function(userpath,forcings){

  rm(list=ls())       # Clean workspace

  cat('Mussel bioenergetic population model\n')
  cat(" \n")

  # Run the preprocessor for the first time to print to screen parameters and forcing selected
  out_pre<-Mussel_pop_pre(userpath,forcings)

  # While cycle to repeat the pre-processing until correct inputs are inserted
  selector="y"

  while (identical(selector,"y")=="TRUE") {
    cat(" \n")
    selector=readline("Do you want to change the inputs? [y/n]")

    if (identical(selector,"n")=="TRUE") {break}

    cat(" \n")
    cat("Insert forcings and parameters in the following folder\n")
    cat(paste0(userpath,"/Mussel_population/Inputs\n"))
    cat(" \n")
    cat("Type y if you entered the correct inputs\n")
    cat("The data will be preprocessed again")
    selector=readline(" ")

    out_pre<-Mussel_pop_pre(userpath,forcings)
    selector="y"
  }

  # Extract preprocessor outputs
  Param=out_pre[[1]]
  times=out_pre[[2]]
  Dates=out_pre[[3]]
  IC=out_pre[[4]]
  Tint=out_pre[[5]]
  Phyint=out_pre[[6]]
  DTint=out_pre[[7]]
  POCint=out_pre[[8]]
  Ccont=out_pre[[9]]
  Ncont=out_pre[[10]]
  Pcont=out_pre[[11]]
  POMint=out_pre[[12]]
  TSSint=out_pre[[13]]
  N=out_pre[[14]]
  CS=out_pre[[15]]


  # Solves ODE
  out_RKsolver<-Mussel_pop_loop(Param, times, IC, Tint, Phyint, DTint, POCint, Ccont, Ncont, Pcont, POMint, TSSint,N,userpath)

  # Post-process data
  out_post<-Mussel_pop_post(userpath, out_RKsolver, times, Dates,N,CS)

  cat(" ")
  cat("End")

  return(out_post)

}