R/mice-resources.R

In roliveros-ramos/mice: Yet another Model of Intermediate Complexity for Ecosystem assessment

.checkResourceBiomass = function(biomass, ndtPerYear, subDtPerYear, T) {

  ndt  = ndtPerYear*T
  Ndt  = subDtPerYear*T
  xdt  = subDtPerYear/ndtPerYear

  if(is.null(biomass))
    stop("Biomass for each resource must be provided, check resources definition.")

  if(length(biomass) == 1) return(rep(biomass, Ndt))

  if(length(biomass) == Ndt) return(biomass)

  if(length(biomass) == ndt) return(rep(biomass, each=xdt))

  if(length(biomass) > ndt) {
    warning(sprintf("Ignoring additional biomass values (%s supplied, %s needed).",
                    length(biomass), ndt))
    return(rep(biomass[seq_len(ndt)], each=xdt))
  }

  stop("One resource biomass value for every time step or a single one must be provided.")

  return(out) # a vector of length T*subDtPerYear

}


getResources = function(groups) {

  isResource = which(sapply(groups, FUN="[", i="type") == "resource")
  groups = groups[isResource]
  ngroups = sapply(groups, FUN="[[", i="ngroups")
  biomass = sapply(groups, FUN="[[", i="biomass")
  biomass = apply(biomass, 1, rep.int, times=ngroups)
  biomass = biomass/rep.int(ngroups, times=ngroups)
  return(1e6*biomass)

}

updateResources = function(x, resources, isResource) {
  x[isResource] = resources
  return(x)
}