R/path-simulation-internal.R

In imarpe/path: Pelagic Assessment Tools for Hydroacoustics

.simulatedPopulation = function(C = numeric(), sp = "anchoveta", ages = NULL, n = 200, sd=0.1, 
                                prob = TRUE){
  
  info = getSpeciesInfo(sp)
  
  k         = info$k
  Linf      = info$Linf
  t0        = info$t0
  longevity = info$longevity
  nRec      = info$nRec
  dL        = info$bin

  if(length(C) == 0 & is.null(ages))
    stop("Al menos 'ages' o 'C' deben tener un valor definido.") 

  if(!is.null(ages)){
    C <- length(ages)
  }else{
    age = runif(1, min=0, longevity)
    ages = seq(from = age, by = 1/nRec, len = C) %% longevity
  }
  
  ages <- sort(unique(ages))
  
  marcas = .createMarks(info)
  
  #N = diff(sort(c(0, runif(length(ages)-1), 1)))
  N = rtruncnorm(n = length(ages), a = 0, b = 1, mean = 0.5, sd = 0.25)
  L = Linf*(1-exp(-k*(ages-t0)))
  S = sd*L # to improve
  
  ind = sample(length(L), size = n*length(L), prob=N, replace=TRUE)
  
  x = rnorm(n*length(L), mean=L[ind], sd=S[ind])
  
  bins = c(union(marcas - 0.5*dL, marcas + 0.5*dL), Inf)
  
  Nil = table(cut(x, breaks = bins, useNA = FALSE, labels = c(marcas, Inf)))
  Pil = Nil/sum(Nil)
  
  output = if(isTRUE(prob)) Pil else Nil
  
  return(output)
}