R/get_fcl.R

In Jpomz/IGPtoy: Simulate Intraguild Predation Dynamics in Three Species Community

#' Calculate Food chain length
#'
#' @description Internal function used by `igp_sim()` to caluclate food chain length in a patch
#'
#' @param N Matrix where rows (`n=3`) are abundances for species B, C and P, and columns (`n = n_patch`) describe each patch in the simulation
#' @param lambda_b Proportion of B in P's diet.
#'
#' @return `fcl` numeric vector of length = `n_patch` describing food chain length in each patch
#' @export
#'
#' @examples
get_fcl <- function(N, lambda_b){
  if(!is.matrix(N)){
    stop("get_fcl() requires N to be a matrix")
  }
  if(ncol(N) != length(lambda_b)){
    stop("get_fcl() requires obs_P_pref to be same length as n_patch in N")
  }
  N[,N[1,] == 0] <- 0
  N[N>0] = 1
  fcl = colSums(N)
  delta  = lambda_b[which(colSums(N)==3)]
  fcl[which(colSums(N)==3)] = delta * 2 + (1 - delta) *3
  fcl
}