F_abundance: F_abundance

In polehalieutique/demerstem: This package aims to falicitate Fish stock assessement for west african partners involved in the EU DEMERSTEM project

F_abundance

Description

F_abundance returns abundance of a class age

Usage

F_abundance(indice)

Arguments

indice

class age

Examples

#' Mat_Cage <- apply(Mat_C, 1, sum) # catch sum by age over fleets
Mat_M <- rep(0.2, age)
age <- length(Mat_M) # number of age class
Mat_N2 <- rep(NA,age) # initial abundance
nb_flot <- length(Mat_C) # number of gear
assign('nb_flot', nb_flot, envir=globalenv())
Mat_q <- Mat_C #initialisation des capturabilites par les captures
indice <- 1 # age de recrutement

# furst calcul of F, q and N from R, C, E and M.
Mat_F2 <- Mat_C/Mat_Cage #  initialisation of F with a ration by gear
indice <- 1
assign('indice', 1, envir=globalenv())
Mat_N2[indice] <- Rinit
assign('Mat_N2', Mat_N2, envir=globalenv())
Mat_F2[indice,] <- Mat_F2[indice,]*optimize(F_a_min, interval=c(0,2))$minimum
assign('Mat_F2', Mat_F2, envir=globalenv())
print(Mat_F2[indice,])
Mat_q[indice,] <- Mat_F2[indice,]/Mat_E[1,]
assign('Mat_q', Mat_q, envir=globalenv())
Mat_N2[indice+1] <- F_abundance(indice)
assign('Mat_N2', Mat_N2, envir=globalenv())

for(compteur in 2:(age)){
  indice <- compteur
  assign('indice', indice, envir=globalenv())

  Mat_F2[indice,] <- Mat_F2[indice,]*optimize(F_a_min, interval=c(0,2))$minimum
  assign('Mat_F2', Mat_F2, envir=globalenv())
  Mat_q[indice,] <- Mat_F2[indice,]/Mat_E[1,]
  assign('Mat_q', Mat_q, envir=globalenv())

  if (indice<age) {
    Mat_N2[indice+1] <- F_abundance(indice)
    assign('Mat_N2', Mat_N2, envir=globalenv())
  }
  if (nb_flot<2) {
    Mat_F2[age,] # si 1 seul engin
  }
  else
  {
    apply(Mat_F2[age,], 1, sum) # si multi-engins
  }
}

polehalieutique/demerstem documentation built on Aug. 4, 2024, 5:12 a.m.