R/Bass_pop_main.R

#' Seabass bioenergetic population model
#'
#' @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] and feeding rate [g/individual x d]
#' @return A list containing model outputs: weight, excreted quantities and quantities to waste, actual and potential ingestion, temperature limitation functions and metabolic rates
#' @export
#'
#' @import matrixStats plotrix rstudioapi
#'

Bass_pop_main<-function(userpath,forcings){

  rm(list=ls())           # Clean workspace

  cat('Sea Bass population bioenergetic model\n')
  cat(" \n")

  currentpath=getwd() # Save current working directory path

  # Run the preprocessor for the first time to print to screen parameters and forcing selected
  out_pre<-Bass_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,"/Bass_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<-Bass_pop_pre(userpath,forcings)
    selector="y"
  }

  # Extract preprocessor outputs
  Param=out_pre[[1]]
  Tint=out_pre[[2]]
  Gint=out_pre[[3]]
  Food=out_pre[[4]]
  IC=out_pre[[5]]
  times=out_pre[[6]]
  Dates=out_pre[[7]]
  N=out_pre[[8]]
  CS=out_pre[[9]]

  # Manages population
  out_RKsolver<-Bass_pop_loop(Param, Tint, Gint, Food, IC, times, N, userpath)

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

  cat(" ")
  cat("End")

  return(out_post)


}

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RAC documentation built on May 2, 2019, 3:26 a.m.