R/RcppExports.R

In LeMaRns: Length-Based Multispecies Analysis by Numerical Simulation

# Generated by using Rcpp::compileAttributes() -> do not edit by hand
# Generator token: 10BE3573-1514-4C36-9D1C-5A225CD40393

#' @title Calculate predation mortality
#'
#' @description Calculates the predation mortality for each species in each length class.
#' @param N A matrix with dimensions \code{nsc} and \code{nfish} representing the number of individuals in each length class for the current time step.
#' @param ration A matrix with dimensions \code{nsc} and \code{nfish} representing the amount of food required for fish of a given species and length class to grow according to the von Bertalanffy growth curve in a time step.
#' @param wgt A matrix with dimensions \code{nsc} and \code{nfish} representing the weight of each species in each length class.
#' @param nfish A numeric value representing the number of species in the model.
#' @param nsc A numeric value representing the number of length classes in the model.
#' @param other A numeric value representing the amount of other food (g) available from prey that is not explicitly represented in the model.
#' @param sc_Linf A numeric vector of length \code{nsc} representing the length class at which each species reaches its asymptotic length.
#' @param suit_M2 A list object of length \code{nfish}. Each element in the list is an array of dimensions \code{nsc}, \code{nsc} and \code{nfish} containing a value between zero and 1 representing prey preference and prey suitability for each species and length class.
#' @details The predation mortality of the \code{i}th species in the \code{j}th length class is
#' @details \code{sum_m(sum_n(I[j,i]*N[j,i]*suit_M2[[m]][n,j,i]/}
#' @details \code{(sum_k(sum_l(suit_M2[[m]][n,l,k]wgt[l,k]N[l,k]))+other)))}
#' @details where \code{sum_m} represents the sum over all \code{m}, \code{sum_n} represents the sum over all \code{n}, \code{sum_l} represents the sum over all \code{l} and \code{sum_k} represents the sum over all \code{k}. This equation corresponds to a Holling type-II functional response. See equation 8 of Hall et al. (2006) for more details.
#' @return A matrix with dimensions \code{nsc} and \code{nfish} representing the the predation mortality for each species in each length class.
#' @references Hall, S. J., Collie, J. S., Duplisea, D. E., Jennings, S., Bravington, M., & Link, J. (2006). A length-based multispecies model for evaluating community responses to fishing. \emph{Canadian Journal of Fisheries and Aquatic Sciences}, 63(6):1344-1359.
#' @examples
#' # Set up the inputs to the function - species-independent parameters
#' nfish <- nrow(NS_par)
#' nsc <- 32
#' maxsize <- max(NS_par$Linf)*1.01 # the biggest size is 1% bigger than the largest Linf
#' l_bound <- seq(0, maxsize, maxsize/nsc); l_bound <- l_bound[-length(l_bound)]
#' u_bound <- seq(maxsize/nsc, maxsize, maxsize/nsc)
#' mid <- l_bound+(u_bound-l_bound)/2
#'
#' # Set up the inputs to the function - species-specific parameters
#' Linf <- NS_par$Linf # the von-Bertalanffy asymptotic length of each species (cm).
#' W_a <- NS_par$W_a # length-weight conversion parameter.
#' W_b <- NS_par$W_b # length-weight conversion parameter.
#' k <- NS_par$k # the von-Bertalnaffy growth parameter.
#' Lmat <- NS_par$Lmat # the length at which 50\% of individuals are mature (cm).
#'
#' # Get phi_min
#' tmp <- calc_phi(k, Linf, nsc, nfish, u_bound, l_bound, calc_phi_min=FALSE,
#'                   phi_min=0.1) # fixed phi_min
#' phi <- tmp$phi
#' phi_min <- tmp$phi_min
#'
#' # Calculate growth increments
#' tmp <- calc_ration_growthfac(k, Linf, nsc, nfish, l_bound, u_bound, mid, W_a, W_b, phi_min)
#' ration <- tmp$ration
#' sc_Linf <- tmp$sc_Linf
#' wgt <- tmp$wgt
#' g_eff <- tmp$g_eff
#'
#' # Calculate predator-prey size preferences
#' prefs <- calc_prefs(pred_mu=-2.25, pred_sigma=0.5, wgt, sc_Linf)
#'
#' # Calculate prey preference and prey suitability
#' suit_M2 <- calc_suit_vect(nsc, nfish, sc_Linf, prefs, NS_tau)
#'
#'
#' # Get an initial population
#' N0 <- get_N0(nsc, nfish, mid, wgt, sc_Linf, intercept=1e10, slope=-5)
#'
#' # Calculate the predation mortality
#' M2 <- calc_M2(N0, ration, wgt, nfish, nsc, other=1e12, sc_Linf, suit_M2)
#' @export
calc_M2 <- function(N, ration, wgt, nfish, nsc, other, sc_Linf, suit_M2) {
    .Call(`_LeMaRns_calc_M2`, N, ration, wgt, nfish, nsc, other, sc_Linf, suit_M2)
}